Compositions for nucleic acid delivery

Abstract

The present invention is based, in part, upon the discovery of charged lipids that provide advantages when used in lipid particles for the in vivo delivery of a therapeutic agent. As such, described herein are compounds useful for delivering a nucleic acid to a cell.

1 . A compound having the formula: 
       
         
           
           
               
               
           
         
       
       wherein:
 R 1  and R 2  are each independently for each occurrence optionally substituted C 10 -C 30  alkyl, optionally substituted C 10 -C 30  alkoxy, optionally substituted C 10 -C 30  alkenyl, optionally substituted C 10 -C 30  alkenyloxy, optionally substituted C 10 -C 30  alkynyl, optionally substituted C 10 -C 30  alkynyloxy, or optionally substituted C 10 -C 30  acyl; 
 
       
         
           
           
               
               
           
         
       
       represents a connection between L 2  and L 1  which is:
 (1) a single bond between one atom of L 2  and one atom of L 1 , wherein
 L 1  is C(R x ) or N; 
 L 2  is —CR 5 R 6 —, —O—, —S—, —N(Q)-, 
 
 
       ═C(R 5 )—, —C(O)N(Q)-, —C(O)O—, —N(Q)C(O)—, —OC(O)—, or —C(O)—;
 (2) a double bond between one atom of L 2  and one atom of L 1 ; wherein
 L 1  is C; 
 L 2  is —CR 5 ═, —N(Q)=, —N—, —O—N═, —N(Q)-N═, or —C(O)N(Q)-N═; 
 
 (3) a single bond between a first atom of L 2  and a first atom of L 1 , and a single bond between a second atom of L 2  and the first atom of L 1 , wherein
 L 1  is C; 
 L 2  has the formula 
 
 
       
         
           
           
               
               
           
         
       
       wherein
   X is the first atom of L 2 , Y is the second atom of L 2 ,   represents a single bond to the first atom of L 1 , and X and Y are each, independently, selected from the group consisting of —O—, —S—, alkylene, —N(Q)-, —C(O)—, —O(CO)—, —OC(O)N(Q)-, —N(Q)C(O)O—, —C(O)O, —OC(O)O—, —OS(O)(Q 2 )O—, and —OP(O)(Q 2 )O—;   Z 1  and Z 4  are each, independently, —O—, —S—, —CH 2 —, —CHR 5 —, or —CR 5 R 5 —;   Z 2  is CH or N;   Z 3  is CH or N;   or Z 2  and Z 3 , taken together, are a single C atom;   A 1  and A 2  are each, independently, —O—, —S—, —CH 2 —, —CHR 5 —, or —CR 5 R 5 —;   each Z is N, C(R 5 ), or C(R 3 );   k is 0, 1, or 2;   each m, independently, is 0 to 5;   each n, independently, is 0 to 5;   where m and n taken together result in a 3, 4, 5, 6, 7 or 8 member ring;   
 (4) a single bond between a first atom of L 2  and a first atom of L 1 , and a single bond between the first atom of L 2  and a second atom of L 1 , wherein 
 (A) L 1  has the formula: 
 
       
         
           
           
               
               
           
         
       
       wherein
   X is the first atom of L 1 , Y is the second atom of L 1 ,   represents a single bond to the first atom of L 2 , and X and Y are each, independently, selected from the group consisting of —O—, —S—, alkylene, —N(Q)-, —C(O)—, —O(CO)—, —OC(O)N(Q)-, —N(Q)C(O)O—, —C(O)O, —OC(O)O—, —OS(O)(Q 2 )O—, and —OP(O)(Q 2 )O—;   T 1  is CH or N;   T 2  is CH or N;   or T 1  and T 2  taken together are C═C;   L 2  is CR 5 ; or   
 (B) L 1  has the formula: 
 
       
         
           
           
               
               
           
         
       
       wherein
   X is the first atom of L 1 , Y is the second atom of L 1 ,   represents a single bond to the first atom of L 2 , and X and Y are each, independently, selected from the group consisting of —O—, —S—, alkylene, —N(Q)-, —C(O)—, —O(CO)—, —OC(O)N(Q)-, —N(Q)C(O)O—, —C(O)O, —OC(O)O—, —O S(O)(Q 2 )O—, and —OP(O)(Q 2 )O—;   T 1  is —CR 5 R 5 —, —N(Q)-, —O—, or —S—;   T 2  is —CR 5 R 5 —, —N(Q)-, —O—, or —S—;   L 2  is CR 5  or N;   
 R 3  has the formula: 
 
       
         
           
           
               
               
           
         
         
           wherein 
         
         each of Y 1 , Y 2 , Y 3 , and Y 4 , independently, is alkyl, cycloalkyl, aryl, aralkyl, or alkynyl; or 
         any two of Y 1 , Y 2 , and Y 3  are taken together with the N atom to which they are attached to form a 3- to 8-member heterocycle; or 
         Y 1 , Y 2 , and Y 3  are all be taken together with the N atom to which they are attached to form a bicyclic 5- to 12-member heterocycle; 
         each R n , independently, is H, halo, cyano, hydroxy, amino, alkyl, alkoxy, cycloalkyl, aryl, heteroaryl, or heterocyclyl; 
         L 3  is a bond, —N(Q)-, —O—, —S—, —(CR 5 R 6 ) a —, —C(O)—, or a combination of any two of these; 
         L 4  is a bond, —N(Q)-, —O—, —S—, —(CR 5 R 6 ) a —, —C(O)—, or a combination of any two of these; 
         L 5  is a bond, —N(Q)-, —O—, —S—, —(CR 5 R 6 ) a —, —C(O)—, or a combination of any two of these; 
         each occurrence of R 5  and R 6  is, independently, H, halo, cyano, hydroxy, amino, alkyl, alkoxy, cycloalkyl, aryl, heteroaryl, or heterocyclyl; or two R 5  groups on adjacent carbon atoms are taken together to form a double bond between their respective carbon atoms; or two R 5  groups on adjacent carbon atoms and two R 6  groups on the same adjacent carbon atoms are taken together to form a triple bond between their respective carbon atoms; 
         each a, independently, is 0, 1, 2, or 3; 
         wherein
 an R 5  or R 6  substituent from any of L 3 , L 4 , or L 5  is optionally taken with an R 5  or R 6  substituent from any of L 3 , L 4 , or L 5  to form a 3- to 8-member cycloalkyl, heterocyclyl, aryl, or heteroaryl group; and 
 any one of Y 1 , Y 2 , or Y 3 , is optionally taken together with an R 5  or R 6  group from any of L 3 , L 4 , and L 5 , and atoms to which they are attached, to form a 3- to 8-member heterocyclyl group; 
 
         each Q, independently, is H, alkyl, acyl, cycloalkyl, alkenyl, alkynyl, aryl, heteroaryl or heterocyclyl; and 
         each Q 2 , independently, is O, S, N(Q)(Q), alkyl or alkoxy. 
       
     
     
         2 . The compound of  claim 1  represented by formula I: 
       
         
           
           
               
               
           
         
       
       wherein,
 X and Y are each independently —O—, —S—, alkylene, —N(Q)-, —C(O)—, —O(CO)—, —OC(O)N(Q)-, —N(Q)C(O)O—, —C(O)O, —OC(O)O—, —OS(O)(Q 2 )O—, or —OP(O)(Q 2 )O—;
 Q is H, alkyl, ω-aminoalkyl, ω-(substituted)aminoalkyl, ω-phosphoalkyl, or ω-thiophosphoalkyl; 
 Q 2  is independently for each occurrence O, S, N(Q)(Q), alkyl or alkoxy; 
 A 1  and A 2  are each independently —O—, —S—, —CH 2 —, —CHR 5 —, —CR 5 R 5 —; 
 Z is N or C(R 3 ); 
 
 each R′, R″, and R″′, independently, is H, alkyl, alkyl, heteroalkyl, aralkyl, cyclic alkyl, or heterocyclyl; 
 R 5  is H, halo, cyano, hydroxy, amino, optionally substituted alkyl, optionally substituted alkoxy, or optionally substituted cycloalkyl; 
 i and j are each independently 0-10; 
 a and b are each independently 0-2; 
 and R 1 , R 2  and R 3  are as defined in  claim 1 . 
 
     
     
         3 . The compound of  claim 2 , selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         4 . The compound of  claim 1  represented by formula XXXIII: 
       
         
           
           
               
               
           
         
       
       wherein,
 E is each independently for each 
 
       occurrence —CH 2 —, —O—, —S—, —SS—, —CO—, —C(O)O—, —C(O)N(R′)—, —OC(O)N(R′)—, —N(R′)C(O)N(R″)—, —C(O)—N(R′)—N═C(R″′)—; —N(R′)—N═C(R″)—, —O—N═C(R″)—, —C(S)O—, —C(S)N(R′)—, —OC(S)N(R′)—, —N(R′)C(S)N(R″)—, —C(S)—N(R′)—N═C(R″′); —S—N═C(R″); —C(O)S—, —SC(O)N(R′)—, —OC(O)—, —N(R′)C(O)—, —N(R′)C(O)O—, —C(R″′)═N—N(R′)—; —C(R″′)═N—N(R′)— C(O)—, —C(R″′)═N—O—, —OC(S)—, —SC (O)—, —N(R′)C(S)—, —N(R′)C(S)O—, —N(R′)C(O)S—, —C(R″′)═N—N(R′)—C(S)—, —C(R″″)═N—S—, C[═N(R′)]O, C[═N(R′)]N(R″), —OC[═N(R′)]—, —N(R″)C[═N(R′)]N(R″′)—, —N(R″)C[═N(R′)]—, 
       
         
           
           
               
               
           
         
       
       arylene, heteroarylene, cycloalkylene, or heterocyclylene;
 each R′, R″, and R″′, independently, is H, alkyl, alkyl, heteroalkyl, aralkyl, cyclic alkyl, or heterocyclyl; 
 and R 1 , R 2  and R 3  are as defined in  claim 1 . 
 
     
     
         5 . The compound of  claim 4 , wherein E is O(CO), (CO)O, OC(O)N(R′), or N(R′)C(O)O. 
     
     
         6 . The compound of  claim 2 , selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         7 . A method for delivering a nucleic acid to a cell comprising contacting cells with a compound according to  claim 1 . 
     
     
         8 . (canceled) 
     
     
         9 . The method of  claim 7 , wherein the composition further comprises a nucleic acid. 
     
     
         10 - 14 . (canceled) 
     
     
         15 . The method of  claim 9 , wherein the nucleic acid includes a chemically modified nucleic acid. 
     
     
         16 - 20 . (canceled) 
     
     
         21 . The method of  claim 9 , wherein the nucleic acid is siRNA. 
     
     
         22 . The method of  claim 9 , wherein the nucleic acid is mRNA. 
     
     
         23 . (canceled) 
     
     
         24 . A storage-stable composition comprising
 a cryoprotectant selected from sucrose, trehalose, glucose, 2-hydroxypropyl-α-cyclodextrin, and sorbitol, and   a compound according to  claim 1 .   
     
     
         25 . The composition of  claim 24 , further comprising a neutral lipid. 
     
     
         26 . The composition of  claim 24 , further comprising a sterol. 
     
     
         27 . The composition of  claim 24 , further comprising a lipid capable of reducing aggregation. 
     
     
         28 . The composition of  claim 24 , further comprising a nucleic acid. 
     
     
         29 . The composition of  claim 24 , wherein the cryoprotectant is present at from 5 wt % to 25 wt %. 
     
     
         30 . The composition of  claim 24 , wherein the cryoprotectant is present at from 7 wt % to 15 wt %. 
     
     
         31 . The composition of  claim 24 , wherein the cryoprotectant includes sucrose. 
     
     
         32 . (canceled) 
     
     
         33 . The composition of  claim 28 , wherein the composition is lyophilized. 
     
     
         34 - 36 . (canceled)