Diarylsulfide backbone containing photolabile protecting groups

Patent metadata

Field	Value
Publication number	US-11001602-B2
Application number	US-201816171970-A
Country	US
Kind code	B2
Filing date	Oct 26, 2018
Priority date	Apr 7, 2011
Publication date	May 11, 2021
Grant date	May 11, 2021

Abstract

The present disclosure relates to photoactivable protecting groups containing a diarylsulfide chromophore, a method for the synthesis thereof and their use as photoactivable protecting groups using maskless photolithography based array synthesis.

First claim

What is claimed is:

1. A method for preparing a diarylsulfide backbone containing one or more photolabile protecting group(s) according to Formula Ib

wherein Y is S or O, and
A is selected from the group consisting of —CH 2 , —CH 2 —CH 2 —, —CH(CH 3 )—, —CH(CH 3 )—CH 2 —, and
R1 is an unsubstituted or substituted aryl- or heteroaryl-group, and R3 is H, a methyl group or an ethyl group, and
wherein R2 is

or wherein R2 is

wherein R4 is H, or R4 with the —O— of Formula III it connects to is a phosphoramidite, H-phosphonate or phosphate triester, and
wherein R5 is H, OH, a halogen or XR6, wherein X is O or S and R6 is H, an alkyl-group, aryl-group, or R6 with the —O— of Formula III it connects to is a phosphoramidite, phosphodiester, phosphotriester, H-phosphonate or an acetal or silicone moiety, and
wherein B is selected from the group consisting of adenine, cytosine, guanine, thymine, uracil, 2,6-diaminopurine-9-yl, hypoxanthin-9-yl, 5-methylcytosinyl-1-yl, 5-amino-4-imidazolecarboxylic acid-1-yl or 5-amino-4-imidazolecarboxylic acid amide-3-yl, wherein when B is adenine, cytosine or guanine the primary amino group optionally has a protecting group or when B is thymine or uracil at the O 4 position is optionally a protecting group, or
wherein R 2 is

wherein R7 is a natural amino acid, a non-natural amino acid or an amino acid derivative, including but not limited to a- or β-amino acids, and formula Ib comprises a urethane bond consisting of a N-terminal nitrogen of R7, the C═O of Formula IV that the N-terminal nitrogen of R7 connects to, and the —O— of formula Ib that the C═O of Formula IV connects to,
or wherein R2 with the —O— of formula Ib it connects to is a natural amino acid, a non-natural amino acid or an amino acid derivative, forming an ester bond to formula Ib, including but not limited to α- or β-amino acids, attached to A by an ester bond comprising the —O— of formula Ib and a C-terminal C═O of R2,
the method comprising the steps of
a) providing p-diethylbenzene as a starting material;
b) bromination of the phenylring;
c) nitration of the obtained compound in Nitric- and Sulfuric Acid in the position para- to the Bromine;
d) purification and crystallization;
e) hydroxymethylation of the compound at the benzylic position;
f) conversion of the aromatic bromine group to the arylsulfide using thiophenol;
g) purification;
h) conversion of the alcohol to chlorocarbonate; and
i) reaction of the chlorocarbonate with a nucleoside and reaction of the nucleoside with a phosphitylating agent, or
reaction of the chlorocarbonate with an amino acid derivative.

2. The method according to claim 1 , characterized in that R1 is a phenyl-group, a tert-butyl-phenyl group, a 1- or 2-naphthyl-group or a 2-pyridyl-group.

3. The method according to claim 1 , characterized in that A is —CH(CH 3 )—CH 2 —.

4. The method according to claim 1 , characterized in that R3 is H or an ethyl group.

5. A method of forming an array through photolithography, said method comprising contacting a substrate having a site activated by exposure to light with a compound of Formula Ib

wherein Y is S or O, and
A is selected from the group consisting of —CH 2 —, —CH 2 —CH 2 —, —CH(CH 3 )—, —CH(CH 3 )—CH 2 —, and
R1 is an unsubstituted or substituted aryl- or heteroaryl-group, and R3 is H, a methyl group or an ethyl group, and
wherein R2 is

or wherein R2 is

wherein R4 is H, or R4 with the —O— of Formula III it connects to is a phosphoramidite, H-phosphonate or phosphate triester, and
wherein R5 is H, OH, a halogen or XR6, wherein X is O or S and R6 is H, an alkyl-group, aryl-group, or R6 with the —O— of Formula III it connects to is a phosphoramidite, phosphodiester, phosphotriester, H-phosphonate or an acetal or silicone moiety, and
wherein B is selected from the group consisting of adenine, cytosine, guanine, thymine, uracil, 2,6-diaminopurine-9-yl, hypoxanthin-9-yl, 5-methylcytosinyl-1-yl, 5-amino-4-imidazolecarboxylic acid-1-yl or 5-amino-4-imidazolecarboxylic acid amide-3-yl, wherein when B is adenine, cytosine or guanine the primary amino group optionally has a protecting group or when B is thymine or uracil at the 0 4 position is optionally a protecting group, or
wherein R2 is

wherein R7 is a natural amino acid, a non-natural amino acid or an amino acid derivative, including but not limited to a- or β-amino acids, and formula Ib comprises a urethane bond consisting of a N-terminal nitrogen of R7, the C═O of Formula IV that the N-terminal nitrogen of R7 connects to, and the —O— of formula Ib that the C═O of Formula IV connects to,
or wherein R2 with the —O— of formula Ib it connects to is a natural amino acid, a non-natural amino acid or an amino acid derivative, forming an ester bond to formula Ib, including but not limited to α- or β-amino acids, attached to A by an ester bond comprising the —O— of formula Ib and a C-terminal C═O of R2.

6. The method of claim 5 wherein the contacting of the substrate with a compound of Formula Ib produces a DNA microarray or a peptide microarray.

7. The method of claim 6 wherein the method produces a DNA microarray.

8. The method of claim 6 wherein the method produces a peptide microarray.

9. The method of claim 5 wherein the substrate and/or the compound is activated by exposure to light between the wavelengths of 374 to 405 nm.

Assignees

• Roche Diagnostics Operations Inc

Inventors

• Stengele Klaus-Peter

Classifications

• Y02P20/55

  Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups · CPC title

• C07H19/02

  sharing nitrogen · CPC title

• C07H19/10

  with the saccharide radical esterified by phosphoric or polyphosphoric acids · CPC title

• C07D235/28

  Sulfur atoms · CPC title

• C07C323/19

  with singly-bound oxygen atoms bound to acyclic carbon atoms of the carbon skeleton · CPC title