Conformationally-preorganized, miniPEG-containing γ-peptide nucleic acids

1. A method for preparing a compound according to Formula I, comprising:

(i) contacting the compound of Formula II

with a compound according to Formula III

to obtain a compound according to Formula IV

(ii) contacting a compound according to Formula V

with a coupling agent; and

(iii) adding the product of step (ii) to the compound according to Formula IV to obtain the compound of Formula I,

wherein

B is a nucleic acid base selected from adenine, guanine, cytosine, thymine or uracil;

Y is selected from the group consisting of bromine, iodine, 4-toluenesulfonate and methanesulfonate;

R 1 , R 2 and R 5 each independently are selected from the group consisting of H, linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxylalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene, −CH 2 (OCH 2 CH 2 ) q OP 1 , −CH 2 —(OCH 2 —CH 2 ) q —NHP 1 , —CH 2 —(OCH 2 —CH 2 ) q —SP 1 , and —CH 2 —(SCH 2 —CH 2 S) q —SP 1 ;

R 3 and R 4 each independently are H;

R 6 is selected from the group consisting of H, linear or branched (C 1 -C 8 )alkyl, substituted or unsubstituted (C 3 -C 8 )aryl and (C 3 -C 8 )aryl(C 1 -C 6 )alkylene;

P is selected from the group consisting of H, 9-fluorenylmethyloxy carbonyl, Boc, benzyloxycarbonyl, tosylate, benzyl, alloc, trityl, benzhydryloxycarbonyl (Bhoc), O-nitroveratryloxycarbonyl (Nvoc), 1-(4,4-dimethyl-2,6-dioxacyclohexylidene)ethyl (Dde), diathiasuccinoyl (Dts), benzothiazole-2-sulfonyl (Bts), dimethoxytrityl and monomethoxytrityl;

P 1 is selected from the group consisting of H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene and (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; and

n and q are independently integers between 1 and 10 inclusive.

2. The method of claim 1 , wherein step (ii) is effected in the presence of a coupling agent in a polar aprotic solvent.

3. The method of claim 1 , wherein the coupling agent is selected from the group consisting of dicyclohexylcarbodiimide, carbonyldiimidazole, O-(benzotriazol-1-yl)-N,N,N′N′-tetramethyluronium hexafluorophosphate (HBTU), (benzotraizol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and O-(7-azabenzotriazol-1-yl)-N,N,N′N′-tetramethyluronium hexafluorophosphate (HATU).

4. The method of claim 1 , further comprising the step of preparing the compound according to Formula III by a method comprising:

(a) contacting

with a CH 3 —(O—CH 2 —CH 2 —) q OX group to obtain

where X is selected from methanesulfonate, 4-toluenesulfonate, or acetyl;

(b) contacting the carboxylic acid group of the product obtained in step (a) with a reducing agent to obtain the corresponding alcohol; and

(c) contacting the alcohol with a reagent to obtain the compound according to Formula III.

5. The method of claim 4 , wherein the reagent in step (c) is selected from the group consisting of methanesulfonyl chloride, 4-toluenesulfonyl chloride and sodium iodide.

6. The method of claim 4 , wherein the contacting step (c) is effected in an aprotic solvent.

7. The method of claim 5 , wherein the reagent is sodium iodide and the contacting step (c) is effected in the presence of a catalyst.

8. The method of claim 7 , wherein the catalyst is zirconium (IV) chloride.

9. A method for synthesizing a peptide nucleic acid (PNA) oligomer having a pre-determined sequence, comprising:

(a) activating the carboxylic acid group of a allyl linker according to Formula VI

(b) contacting a solid support with the activated allyl linker;

(c) activating the carboxylic acid group of a first amino protected PNA monomer or an amino protected γPNA monomer determined by the pre-determined sequence and then contacting the activated carboxylic acid monomer with the product from step (b);

(d) de-protecting the amino group of the product from step (c),

(e) contacting the product from step (d) with a second sequence specific PNA monomer or a γ-PNA monomer;

(f) repeating steps (c), (d) and (e) to synthesize the peptide nucleic acid (PNA) oligomer comprising at least one PNA monomer;

wherein

the γ-PNA monomer is a compound according to Formula I

wherein

B is a nucleic acid base selected from adenine, guanine, cytosine, thymine or uracil;

R 1 , R 2 and R 5 each independently are selected from the group consisting of H, linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene, —CH 2 —(OCH 2 —CH 2 ) q —OP 1 , —CH 2 —(OCH 2 —CH 2 ) q —NHP 1 , —CH 2 —(OCH 2 —CH 2 ) q —SP 1 and —CH 2 —(SCH 2 —CH 2 ) q —SP 1 ;

R 3 and R 4 each independently are H;

R 6 is selected from the group consisting of H, linear or branched (C 1 -C 8 )alkyl, substituted or unsubstituted (C 3 -C 8 )aryl and (C 3 -C 8 )aryl(C 1 -C 6 )alkylene;

P is selected from the group consisting of H, 9-fluorenylmethyloxy carbonyl, Boc, benzyloxycarbonyl, tosylate, benzyl, alloc, trityl, benzhydryloxycarbonyl (Bhoc), O-nitroveratryloxycarbonyl (Nvoc), 1-(4,4-dimethyl-2,6-dioxacyclohexylidene)ethyl (Dde), diathiasuccinoyl (Dts), benzothiazole-2-sulfonyl (Bts), dimethoxytrityl and monomethoxytrityl;

P 1 is selected from the group consisting of H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene and (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; and

n and q are independently integers between 1 and 10 inclusive.

10. The method of claim 9 , wherein steps (a) through (f) are performed using an automated solid-phase synthesizer.

11. A compound according to Formula I

wherein,

B is selected from the group consisting of adenine, cytosine, guanine, thymine, and uracil

P is selected from the group consisting of hydrogen (H), 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc), benzyloxycarbonyl (Cbz), benzyl (Bn), tosylate (Tos), allyloxycarbonyl (alloc), benzhydryloxycarbonyl (Bhoc), 0-nitroveratryloxycarbonyl (Nvoc), 1-(4,4-dimethyl-2,6-dioxacyclohexylidene)ethyl (Dde), diathiasuccinoyl (Dts), benzothiazole-2-sulfonyl (Bts), trityl (Trt), monomethoxytrityl (MMT) and dimethoxytrityl (DMT) group;

each of R 1 and R 2 is independently selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxylalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene,

provided that at least one of R 1 and R 2 is selected from the group consisting of:

each of R 3 and R 4 is independently selected from the group consisting of hydrogen (H),

R 5 is selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxylalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene and (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene;

R 6 is selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, substituted or unsubstituted (C 3 -C 8 )aryl and (C 3 -C 8 )aryl(C 1 -C 6 )alkylene;

P 2 is selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc), benzyloxycarbonyl (Cbz), benzyl (Bn), tosylate (Tos), allyloxycarbonyl (alloc), trityl (Trt), monomethoxytrityl (MMT) and dimethoxytrityl (DMT) group;

P 3 is selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene and (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene;

n is an integer from 1 to 10, inclusive;

x is an integer from 1 to 10, inclusive; and

y is an integer from 1 to 9, inclusive.

12. The compound of claim 11 , wherein

P is selected from the group consisting of hydrogen (H), 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc) and benzyloxycarbonyl (Cbz);

R 1 is selected from the group consisting of —CH 2 —[O(CH 2 ) 2 ] x —OP 3 , —CH 2 —[O(CH 2 ) 2 ] y —NHP 2 , and —CH 2 —[O(CH 2 ) 2 ] y —SP 2 , wherein x and y are independently an integer from 2 to 4, inclusive;

each of R 2 , R 3 and R 4 is hydrogen (H);

P 2 is selected from the group consisting of hydrogen, methyl and ethyl;

P 3 is selected from the group consisting of hydrogen (H), methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl and t-butyl; and

R 6 is selected from the group consisting of hydrogen (H), methyl and ethyl.

13. The compound of claim 11 , wherein

P is selected from the group consisting of hydrogen (H), 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc) and benzyloxycarbonyl (Cbz);

R 2 is selected from the group consisting of —CH 2 —[O(CH 2 ) 2 ] x —OP 3 , —CH 2 —[O(CH 2 ) 2 ] y —NHP 2 , or —CH 2 -—[O(CH 2 ) 2 ] y —SP 2 , wherein x and y are independently an integer from 2 to 4, inclusive;

each of R 1 , R 3 and R 4 is hydrogen (H);

P 2 is selected from the group consisting of hydrogen, methyl or ethyl;

P 3 is selected from the group consisting of hydrogen (H), methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl and t-butyl; and

R 6 is selected from the group consisting of hydrogen (H), methyl and ethyl.

14. The compound of claim 11 , wherein B is selected from the group consisting of adenine, cytosine, and guanine, each comprising a benzyloxycarbonyl (Cbz) protecting group linked to an exocyclic amino group.

15. The compound of claim 11 , wherein

P is selected from the group consisting of 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc) and benzyloxycarbonyl (Cbz);

P 2 is selected from the group consisting of hydrogen, methyl and ethyl;

P 3 is selected from the group consisting of hydrogen (H), methyl and t-butyl;

R 5 is hydrogen (H);

R 6 is selected from the group consisting of hydrogen (H), methyl and ethyl; and

n=1.

16. The compound of claim 11 , wherein the compound has Formula XX,

wherein

P is selected from the group consisting of 9-fluorenylmethyloxycarbonyl (Fmoc) amd t-butyloxycarbonyl (Boc);

x is an integer from 2 to 4 inclusive;

R 7 is selected from the group consisting of hydrogen (H), methyl and ethyl; and

R 8 is selected from the group consisting of hydrogen (H), methyl, ethyl and t-butyl.

17. The compound of claim 16 , wherein x is 2, R 7 is hydrogen or ethyl; and R 8 is t-butyl.

18. The compound of claim 11 , wherein the compound has Formula XXI,

wherein

P is selected from the group consisting of 9-fluorenylmethyloxycarbonyl (Fmoc) and t-butyloxycarbonyl (Boc);

x is an integer from 2 to 4 inclusive;

R 7 is selected from the group consisting of hydrogen (H), methyl and ethyl; and

R 8 is selected from the group consisting of hydrogen (H), methyl, ethyl and t-butyl.

19. The compound of claim 18 , wherein x is 2, R 7 is hydrogen or ethyl; and R 8 is t-butyl.

20. A method for preparing a compound according to Formula IA

comprising:

(i) contacting a compound according to Formula II

with a compound according to Formula III

to obtain a compound according to Formula IV

(ii) contacting a compound according to Formula V

with a coupling agent; and

(iii) adding the product of step (ii) to the compound according to Formula IV to obtain the compound according to Formula IA;

wherein

X is selected from the group consisting of adenine, cytosine, guanine, thymine, and uracil

Y is selected from the group consisting of bromine, iodine, 4-toluenesulfonate and methanesulfonate;

P is selected from the group consisting of hydrogen (H), 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc), benzyloxycarbonyl (Cbz), benzyl (Bn), tosylate (Tos), allyloxycarbonyl (alloc), benzhydryloxycarbonyl (Bhoc), O-nitroveratryloxycarbonyl (Nvoc), 1-(4,4-dimethyl-2,6-dioxacyclohexylidene)ethyl (Dde), diathiasuccinoyl (Dts), benzothiazole-2-sulfonyl (Bts), trityl (Trt), monomethoxytrityl (MMT) and dimethoxytrityl (DMT);

each of R 1 and R 2 is independently selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxylalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene,

each of R 3 and R 4 is independently selected from the group consisting of hydrogen (H),

R 5 is selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxylalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene and (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene;

R 6 is selected from the group consisting of linear or branched (C 1 -C 8 )alkyl, substituted or unsubstituted (C 3 -C 8 )aryl and (C 3 -C 8 )aryl(C 1 -C 6 )alkylene;

P 2 is selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc), benzyloxycarbonyl (Cbz), benzyl (Bn), tosylate (Tos), allyloxycarbonyl (alloc), trityl (Trt), monomethoxytrityl (MMT) and dimethoxytrityl (DMT);

P 3 selected from the group consisting of hydrogen (H), linear or branched (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene and (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene;

n is an integer from 1 to 10, inclusive;

x is an integer from 1 to 10, inclusive; and

y is an integer from 1 to 9, inclusive.

21. The method of claim 20 , wherein at least one of R 1 and R 2 is selected from the group consisting of:

22. The method of claim 20 , wherein in step (ii) the coupling agent is selected from the group consisting of dicyclohexylcarbodiimide (DCC), carbonyldiimidazole (CDI), O-(benzotriazol-1-yl)-N,N,N′N′-tetramethyluronium hexafluorophosphate (HBTU), (benzotraizol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and O-(7-azabenzotriazol-1-yl)-N,N,N′N′-tetramethyluronium hexafluorophosphate (HATU).

23. The method of claim 20 , further comprising; (iv) saponifying the compound according to Formula I to obtain a compound according to Formula XI:

wherein,

X, P, R 1 , R 2 , R 3 , R 4 , R 5 , P 2 , P 3 , n, x, y are as recited in claim 21 .

24. The method of claim 23 , wherein the compound according to Formula IX has the following formula:

wherein

P is selected from the group consisting of 9-fluorenylmethyloxycarbonyl (Fmoc) and t-butyloxycarbonyl (Boc);

x is an integer from 2 to 4 inclusive; and

R 8 is selected from the group consisting of hydrogen (H), methyl, ethyl and t-butyl.

25. The method of claim 23 , wherein the compound of Formula IX has the following formula:

wherein

P is selected from the group consisting of 9-fluorenylmethyloxycarbonyl (Fmoc) and t-butyloxycarbonyl (Boc);

x is an integer from 2 to 4 inclusive; and

R 8 is selected from the group consisting of hydrogen (H), methyl, ethyl and t-butyl.

26. The method of claim 23 , wherein X is selected from the group consisting of adenine, cytosine, and guanine, each comprising a benzyloxycarbonyl (Cbz) protecting group linked to an exocyclic amino group.