Processes for preparing phosphorodiamidate morpholino oligomers
Provided herein are processes for preparing an oligomer (e.g., a morpholino oligomer). The synthetic processes described herein may be advantageous to scaling up oligomer synthesis while maintaining overall yield and purity of a synthesized oligomer.
1. A process for preparing an oligomeric compound of Formula (E):
or a pharmaceutically acceptable salt thereof,
wherein the process comprises the sequential steps of:
(a) contacting a compound of Formula (A1):
wherein R 1 is a support-medium and R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl;
with a deblocking agent to form the compound of Formula (II):
wherein R 1 is a support-medium;
(b) contacting the compound of Formula (II) with a compound of Formula (A2):
wherein R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl;
to form a compound of Formula (A3):
wherein R 1 is a support-medium, and R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl;
(c) contacting the compound of Formula (A3) with a deblocking agent to form a compound of Formula (IV):
wherein R 1 is a support-medium;
(d) contacting the compound of Formula (IV) with a compound of Formula (A4):
wherein R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R 4 is
to form a compound of Formula (A5):
wherein R 1 is a support-medium, R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and
R 4 is
(e) performing 29 iterations of the sequential steps of:
(e1) contacting the product formed by the immediately prior step with a deblocking agent; and
(e2) contacting the compound formed by the immediately prior step with a compound of Formula (A8):
wherein R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
to form a compound of Formula (A9):
wherein n is 30, R 1 is a support-medium, R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
and
(f) contacting the compound of Formula (A9) with a deblocking agent to form a compound of Formula (A10):
wherein n is 30, R 1 is a support-medium, and R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
(g) contacting the compound of Formula (A10) with a cleaving agent to form a compound of Formula (A11):
wherein n is 30, and R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
and
(h) contacting the compound of Formula (A11) with a deprotecting agent to form the oligomeric compound of Formula (E).
2. The process of claim 1 , wherein the compound of Formula (A4) is of Formula (A4a):
wherein:
R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and
R 4 is
3. The process of claim 1 , wherein the compound of Formula (A5) is of Formula (A5a):
wherein:
R 1 is a support-medium
R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and
R 4 is
4. The process of claim 1 , wherein the compound of Formula (A8) is of Formula (A8a):
wherein:
R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and
R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
5. The process of claim 1 , wherein the compound of formula (A9) is of Formula (A9a):
wherein:
n is 30,
R 1 is a support-medium,
R 3 is selected from the group consisting of trityl, monomethoxytrityl, dimethoxytrityl and trimethoxytrityl, and
R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
6. The process of claim 1 , wherein the compound of Formula (A10) is of Formula (A10a):
wherein:
n is 30,
R 1 is a support-medium, and
R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
7. The process of claim 1 , wherein the compound of Formula (A11) is of Formula (A11a):
wherein:
n is 30, and
R 4 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
8. The process of claim 1 , wherein the oligomeric compound of Formula (E) is an oligomeric compound of Formula (XII):
or a pharmaceutically acceptable salt thereof.
9. The process of claim 1 , wherein the process comprises the sequential steps of:
(a) contacting a compound of Formula (I):
wherein R 1 is a support-medium,
with a deblocking agent to form the compound of Formula (II):
wherein R 1 is a support-medium;
(b) contacting the compound of Formula (II) with compound (B):
to form a compound of Formula (III):
wherein R′ is a support-medium;
(c) contacting the compound of Formula (III) with a deblocking agent to form a compound of Formula (IV):
wherein R′ is a support-medium;
(d) contacting the compound of Formula (IV) with a compound of Formula (C):
to form a compound of Formula (V):
wherein R 1 is a support-medium;
(e) contacting the compound of Formula (V) with a deblocking agent to form a compound of Formula (VI):
wherein R′ is a support-medium;
(f) contacting the compound of Formula (VI) with compound of Formula (F):
to form a compound of Formula (VII):
wherein R′ is a support-medium;
(g) performing 28 iterations of the sequential steps of:
(g1) contacting the product formed by the immediately prior step with a deblocking agent; and
(g2) contacting the compound formed by the immediately prior step with a compound of Formula (VIII):
wherein R 1 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
wherein, for each iteration from 1 to 28, R 1 is:
Iteration No.
R 2
1
PC
2
PC
3
PA
4
PA
5
PC
6
PA
7
T
8
PC
9
PA
10
PA
11
DPG
12
DPG
13
PA
14
PA
15
DPG
16
PA
17
T
18
DPG
19
DPG
20
PC
21
PA
22
T
23
T
24
T
25
PC
26
T
27
PA
28
DPG
to form a compound of Formula (IX):
wherein R 1 is a support-medium,
wherein R 2 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
and
wherein R 2 is at each position from 1 to 30 and 5′ to 3′:
Position No. 5′ to 3′
R 2
1
PC
2
T
3
PC
4
PC
5
PA
6
PA
7
PC
8
PA
9
T
10
PC
11
PA
12
PA
13
DPG
14
DPG
15
PA
16
PA
17
DPG
18
PA
19
T
20
DPG
21
DPG
22
PC
23
PA
24
T
25
T
26
T
27
PC
28
T
29
PA
30
DPG
(h) contacting the compound of Formula (IX) with a deblocking agent to form a compound of Formula (X):
wherein R 1 is a support-medium,
wherein R 2 is, as per the oligomeric compound of Formula (E), selected from the group consisting of:
and
wherein R 2 is at each position from 1 to 30 and 5′ to 3′:
Position No. 5′ to 3′
R 2
1
PC
2
T
3
PC
4
PC
5
PA
6
PA
7
PC
8
PA
9
T
10
PC
11
PA
12
PA
13
DPG
14
DPG
15
PA
16
PA
17
DPG
18
PA
19
T
20
DPG
21
DPG
22
PC
23
PA
24
T
25
T
26
T
27
PC
28
T
29
PA
30
DPG
(i) contacting the compound of Formula (X) with a cleaving agent to form a compound of Formula (XI):
wherein R 2 is, as per the oligomeric compound of Formula (E), from the group consisting of:
and
wherein R 2 is at each position from 1 to 30 and 5′ to 3′:
Position No. 5′ to 3′
R 2
1
PC
2
T
3
PC
4
PC
5
PA
6
PA
7
PC
8
PA
9
T
10
PC
11
PA
12
PA
13
DPG
14
DPG
15
PA
16
PA
17
DPG
18
PA
19
T
20
DPG
21
DPG
22
PC
23
PA
24
T
25
T
26
T
27
PC
28
T
29
PA
30
DPG
and
(j) contacting the compound of Formula (XI) with a deprotecting agent to form the oligomeric compound of claim 1 .
10. The process of claim 1 , wherein step (d) or step (e2) further comprises contacting the compound of Formula (IV) or the compound formed by the immediately prior step, respectively, with a capping agent.
11. The process of claim 1 , wherein the deblocking agent used in each step is halogenated acid or cyanoacetic acid.
12. The process of claim 11 , wherein the halogenated acid is selected from the group consisting of chloroacetic acid, dichloroacetic acid, trichloroacetic acid, fluoro acetic acid, difluoroacetic acid, and trifluoroacetic acid.
13. The process of claim 1 , wherein at least one of steps (a), (c), (e1), and (f) further comprise the step of contacting the deblocked compound of each step with a neutralization agent.
14. The process of claim 1 , wherein the support-medium comprises a material selected from the group consisting of glass, modified or functionalized glass, plastics, polysaccharides, nylon or nitrocellulose, ceramics, resins, silica, silica-based materials, carbon, metals, and optical fiber bundles.
15. The process of claim 14 , wherein plastics are chosen from acrylics, polystyrene, copolymers of styrene, polypropylene, polyethylene, polybutylene, polyurethanes, or polytetrafluoroethylene.
16. The process of claim 15 , wherein polystyrene is polystyrene with 1% crosslinked divinylbenzene.