JPWO2020191252A5

JPWO2020191252A5 -

Info

Publication number: JPWO2020191252A5
Application number: JP2021556501A
Authority: JP
Publication date: 2023-12-22

Claims

Steps below:
(1) Coupling step;
(2) optionally a pre-modification capping step;
(3) Modification step;
(4) optionally a post-modification capping step; and (5) optionally one or more cycles each independently comprising a deblocking step, the method comprising:
In at least one cycle, the coupling step independently comprises reacting a free hydroxyl group of the oligonucleotide or nucleoside with a coupling partner compound ;
The modification step includes sulfidation, the sulfidation includes converting a -P(-)-bonded phosphorus atom to a -P(=S)(-)-bonded phosphorus atom,
The modification step includes converting a -P(-)-bonded phosphorus atom to a -P(=N-)(-)-bonded phosphorus atom,
Each partner compound containing a chiral auxiliary group is independently
(In the formula,
BA is a C _3-30 alicyclic group, a C _6-30 aryl, a C _5-30 heteroaryl having 1 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon; , a C _3-30 heterocyclyl having 1 to 10 heteroatoms independently selected from , oxygen, nitrogen, sulfur, phosphorous and silicon, natural nucleobase moieties, and modified nucleobase moieties. is a group substituted with;
Each of R ^2s and R ^4s is independently R ^s ;
Each R ^s independently represents -H, halogen, -CN, -N ₃ , -NO, -NO ₂ , -L ^s -R', -L ^s -Si(R) ₃ , -L ^s -OR' , -L ^s -SR', -L ^s -N(R') ₂ , -OL ^s -R', -OL ^s -Si(R) ₃ , -OL ^s -OR', - OL ^s -SR' or -OL ^s -N(R') ₂ ;
R ² is -CH ₂ SO ₂ R', where R' is C _1-30 aliphatic, C _1-30 heteroaliphatic with 1-10 heteroatoms , C _6-30 aryl , C _6-30 arylaliphatic, C 6-30 arylheteroaliphatic with 1-10 heteroatoms _, 5-30 membered heteroaryl with 1-10 heteroatoms and 1-10 heteroatoms. an optionally substituted group selected from 3-30 membered heterocyclyl having
Each L ^s independently has a covalent bond or a C _1-30 aliphatic group and _1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. a divalent optionally substituted straight-chain or branched group selected from group groups, wherein one or more methylene units are optionally and independently C _1-6 alkylene, C _1-6 alkenylene, -C≡C-, a divalent C ₁ -C ₆ heteroaliphatic group containing 1 to 5 members independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. Divalent C ₁ -C ₆ heteroaliphatic group having a heteroatom, -C(R') ₂ -, -Cy-, -O-, -S-, -S-S-, -N(R') -, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R' )-, -N(R')C(O)O-, -S(O)-, -S(O) ₂ -, -S(O) ₂ N(R')-, -C(O)S -, -C(O)O-, -P(O)(OR')-, -P(O)(SR')-, -P(O)(R')-, -P(O)(NR ')-, -P(S)(OR')-, -P(S)(SR')-, -P(S)(R')-, -P(S)(NR')-, -P (R')-, -P(OR')-, -P(SR')-, -P(NR')-, -P(OR') [B(R') 3 ]-, -OP ₍ O )(OR')O-, -OP(O)(SR')O-, -OP(O)(R')O-, -OP(O)(NR')O-, -OP(OR') selected from O-, -OP(SR')O-, -OP(NR')O-, -OP(R')O-, or -OP(OR') [B(R') ₃ ]O- , is replaced by an optionally substituted group, and one or more carbon atoms are optionally and independently replaced with Cy ^L ;
Each -Cy- independently carries a C _3-20 alicyclic ring, a C _6-20 aryl ring, and 1 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus, and silicon. and a 3-20 membered heterocyclyl ring having 1 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. is a divalent group;
Each Cy ^L independently has a C _3-20 alicyclic ring, a C _6-20 aryl ring, and 1 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus, and silicon. an optionally substituted group selected from 5-20 membered heteroaryl rings and 3-20 membered heterocyclyl rings having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. is a tetravalent group;
each R' is independently -R, -C(O)R, -C(O)OR or -S(O) _2R ;
Each R is independently -H or C _1-30 aliphatic and C 1-30 heteroaliphatic having 1 _to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. , C _6-30 aryl, C _6-30 arylaliphatic, and C _6-30 arylheteroaliphatic having 1 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. , 5-30 membered heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon; and 1-30 membered heteroaryl independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. an optionally substituted group selected from 3-30 membered heterocyclyl having 10 heteroatoms, or
The two R groups optionally and independently take together to form a covalent bond, or;
Two or more R groups on the same atom optionally and independently together with said atom contain from 0 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. forming an optionally substituted 3- to 30-membered monocyclic, bicyclic or polycyclic ring having in addition to said atoms; or
Two or more R groups on two or more atoms, optionally and independently together with their intervening atoms, are 0 to 10 independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. forming an optionally substituted 3- to 30-membered monocyclic, bicyclic, or polycyclic ring having, in addition to the intervening atoms,
or a salt thereof .

2. The method of claim 1 , wherein in the partner compound R ^4s is -H.

3. The method of claim 2 , wherein in the partner compound R ^2s is -H.

3. The method of claim 2 , wherein in the partner compound R ^2s is -OR, where R is an optionally substituted C _1-6 aliphatic.

3. The method of claim 2 , wherein in the partner compound R ^2s is -O-Si(R) ₃ , where each R is independently not -H.

A method according to any one of claims 1 to 5 , wherein R ² is -CH ₂ SO ₂ R', where R' is optionally substituted phenyl .

A method according to any one of claims 1 to 5 , wherein R ² is -CH ₂ SO ₂ R', where R' is phenyl .

A method according to any one of claims 1 to 5 , wherein R ² is -CH ₂ SO ₂ R', where R' is tert-butyl .

A method according to any one of claims 1 to 8 , comprising removing the chiral auxiliary group by contacting the oligonucleotide containing the chiral auxiliary group with a base under anhydrous conditions.

10. The method of claim 9 , wherein the base is DEA.

The product oligonucleotide has a phosphorothioate internucleotide linkage , or
The method according to any one of claims 1 to 10 , comprising a sugar containing 2'-OH .

12. The method of claim 11 , wherein the product oligonucleotide further comprises a non-negatively charged internucleotide linkage.

13. The method of claim 12 , wherein the non-negatively charged internucleotide bond is n001.

12. The method of claim 11 , wherein the product oligonucleotide further comprises a natural phosphate linkage.

An oligonucleotide, comprising an internucleotide linkage of ^*P S or ^*P R,
^* PS is independently the formula
or its salt form,
^*PR is independently the formula
or its salt form,
further comprising an internucleotide bond of ^*N S or ^*N R;
^* NS is independently the formula
or its salt form, where P=W ^N is P ^N ,
^* NR is independently the formula
or its salt form, where P=W ^N is P ^N ,
In the formula, -X-Ls-R ⁵ is
and
where R ⁴ and R ⁵ together with their intervening atoms represent an optionally substituted 3- to 20-membered monocyclic, bicyclic or polycyclic ring having 1 to 5 heteroatoms. forming a cyclic ring,
R ⁶ is -C(O)R', where R' is independently -R, -C(O)R, -C(O)OR or -S(O) _2R ,
R ² is -CH ₂ SO ₂ R', where R' is C _1-30 aliphatic, C _1-30 heteroaliphatic with 1-10 heteroatoms , C _6-30 aryl , C _6-30 arylaliphatic, C 6-30 arylheteroaliphatic with 1-10 heteroatoms _, 5-30 membered heteroaryl with 1-10 heteroatoms and 1-10 heteroatoms. an optionally substituted group selected from 3-30 membered heterocyclyl having
P ^N is P (=N-L-R ⁵ ),
And;
Q ^- is an anion;
Each R ^s is independently -H, halogen, -CN, -N ₃ , -NO, -NO ₂ , -L ^s -R', -L ^s -Si(R') ₃ , -L ^s -OR ', -L ^s -SR', -L ^s -N(R') ₂ , -OL ^s -R', -OL ^s -Si(R) ₃ , -OL ^s -OR', -OL ^s -SR' or -OL ^s -N(R') ₂ ;
g is 0 to 20;
Ring A ^L is an optionally substituted 3- to 20-membered monocyclic, bicyclic or It is a polycyclic ring;
Each of R ¹ is independently -H, -L ^s -R', halogen, -CN, -NO ₂ , -L ^s -Si(R') ₃ , -OR', -SR' or -N( R') ₂ ;
Each of X, Y and Z is independently -O-, -S-, -N(-L ^s -R ¹ )-, or L ^s ;
Each of L and L ^b is independently L ^s ;
Each L ^s independently has a covalent bond or a C _1-30 aliphatic group and _1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. a divalent optionally substituted straight-chain or branched group selected from group groups, wherein one or more methylene units are optionally and independently C _1-6 alkylene, C _1-6 alkenylene, -C≡C-, a divalent C ₁ -C ₆ heteroaliphatic group containing 1 to 5 members independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. Divalent C ₁ -C ₆ heteroaliphatic group having a heteroatom, -C(R') ₂ -, -Cy-, -O-, -S-, -S-S-, -N(R') -, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R' )-, -N(R')C(O)O-, -S(O)-, -S(O) ₂ -, -S(O) ₂ N(R')-, -C(O)S -, -C(O)O-, -P(O)(OR')-, -P(O)(SR')-, -P(O)(R')-, -P(O)(NR ')-, -P(S)(OR')-, -P(S)(SR')-, -P(S)(R')-, -P(S)(NR')-, -P (R')-, -P(OR')-, -P(SR')-, -P(NR')-, -P(OR') [B(R') 3 ]-, -OP ₍ O )(OR')O-, -OP(O)(SR')O-, -OP(O)(R')O-, -OP(O)(NR')O-, -OP(OR') selected from O-, -OP(SR')O-, -OP(NR')O-, -OP(R')O-, or -OP(OR') [B(R') ₃ ]O- , is replaced by an optionally substituted group, and one or more carbon atoms are optionally and independently replaced with Cy ^L ;
Each R' is independently -R, -C(O)R, -C(O)OR or -S(O) ₂ R, unless otherwise specified;
Each R is independently -H or C _1-30 aliphatic and C 1-30 heteroaliphatic having 1 _to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. , C _6-30 aryl, C _6-30 arylaliphatic, and C _6-30 arylheteroaliphatic having 1 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. , 5-30 membered heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon; and 1-30 membered heteroaryl independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. an optionally substituted group selected from 3-30 membered heterocyclyl having 10 heteroatoms, or
the two R groups optionally and independently together form a covalent bond, or;
Two or more R groups on the same atom optionally and independently together with that atom contain from 0 to 10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. forms an optionally substituted 3- to 30-membered monocyclic, bicyclic or polycyclic ring having in addition to that atom; or
0 to 10 in which two or more R groups on two or more atoms are optionally and independently together with their intervening atoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon. forming an optionally substituted 3- to 30-membered monocyclic, bicyclic or polycyclic ring having in addition to intervening atoms,
oligonucleotide.

16. The oligonucleotide of claim 15, wherein R ² is -CH ₂ SO ₂ R', R' is optionally substituted phenyl , or R' is tert-butyl . .

16. The oligonucleotide of claim 15, wherein R ² is -CH ₂ SO ₂ R', R' is optionally substituted phenyl, or R' is phenyl.

providing an oligonucleotide according to any one of claims 15 to 17, and a chiral auxiliary group -X-Ls-R ^５5 A method comprising the step of removing.

19. The method of claim 18, wherein the base is DEA.