Preparation of lipid nanoparticles and methods of administration thereof

1. A method of producing a lipid nanoparticle (LNP) composition, the method comprising:

ia) converting a water-soluble salt of a nucleic acid to an organic solvent-soluble nucleic acid prior to the mixing;

i) mixing an aqueous buffer solution and the organic solution, thereby forming a lipid nanoparticle (LNP) formulation comprising a lipid nanoparticle (LNP) encapsulating the nucleic acid; and

ii) processing the lipid nanoparticle (LNP) formulation, thereby forming the lipid nanoparticle composition;

wherein the organic solution comprises the organic solvent-soluble nucleic acid and an ionizable lipid in the organic solvent,

wherein the organic solvent comprises ethanol and benzyl alcohol; and

wherein the organic solvent-soluble nucleic acid comprises an organic cation.

2. The method of claim 1 , further comprising:

iaa) lyophilizing the organic solvent-soluble nucleic acid after step ia).

3. The method of claim 1 , wherein the mixing in step i) comprises turbulent mixing, laminar mixing, or microfluidic mixing.

4. The method of claim 1 , wherein converting in step ia) comprises at least one step selected from the group consisting of dialysis, tangential flow filtration (TFF), hydrophobic ion pairing reverse phase chromatography, ion exchange chromatography, and size exclusion chromatography.

5. The method of claim 1 , wherein the cation is a tertiary amine cation.

6. The method of claim 1 , wherein the organic cation is at least one selected from the group consisting of tributylamine cation (TBA), tripropylamine (TPA) cation, and triethylamine (TEA) cation.

7. The method of claim 1 , wherein the water-soluble salt of a nucleic acid is selected from the group consisting of a sodium salt and a tris(hydroxymethyl)aminomethane (Tris) salt.

8. The method of claim 1 , wherein the organic solution further comprises a wetting agent.

9. The method of claim 1 , wherein the aqueous buffer solution is at least one buffer selected from the group consisting of an acetate buffer, citrate buffer, phosphate buffer, and a tris buffer.

10. The method of claim 1 , wherein the organic solution further comprises an encapsulation agent, wherein the encapsulation agent is

1) a compound of Formula (EA-I):

or a salt or an isomer thereof, wherein

R 201 and R 202 are each independently selected from the group consisting of H, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, and (C═NH)N(R 101 ) 2 wherein each R 101 is independently selected from the group consisting of H, C 1 -C 6 alkyl, and C 2 -C 6 alkenyl;

R 203 is selected from the group consisting of C 1 -C 20 alkyl and C 2 -C 20 alkenyl;

R 204 is selected from the group consisting of H, C 1 -C 20 alkyl, C 2 -C 20 alkenyl, C(O)(OC 1 -C 20 alkyl), C(O)(OC 2 -C 20 alkenyl), C(O)(NHC 1 -C 20 alkyl), and C(O)(NHC 2 -C 20 alkenyl);

n1 is selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10;

2) a compound of Formula (EA-II)

or a salt or an isomera thereof, wherein

X 101 is a bond, NH, or O;

R 101 and R 102 are each independently selected from the group consisting of H, C 1 -C 6 alkyl, and C 2 -C 6 alkenyl;

R 103 and R 104 are each independently selected from the group consisting of C 1 -C 20 alkyl and C 2 -C 20 alkenyl; and

n1 is selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10; or

3) a compound of Formula (EA-III)

or a salt or an isomer thereof, wherein

R 105 and R 106 are each independently selected from the group consisting of H, C 1 -C 6 alkyl, and C 2 -C 6 alkenyl;

R 107 is selected from the group consisting of C 1 -C 20 alkyl and C 2 -C 20 alkenyl;

R 108 is selected from the group consisting of H and C(O)NR 109 R 110 ;

R 109 and R 110 are each independently selected from the group consisting of H, C 1 -C 6 alkyl, and C 2 -C 6 alkenyl; and

n2 is selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10.

11. The method of claim 1 , wherein the nucleic acid is a messenger RNA (mRNA).

12. The method of claim 1 , wherein the organic solution further comprises a phospholipid, a PEG lipid, a structural lipid or any combination thereof.

13. The method of claim 12 , wherein the LNP formulation and/or LNP composition comprises

about 40-60 mol % ionizable lipid;

about 5-15 mol % phospholipid;

about 35-45 mol % structural lipid; and

about 0.01-2.0 mol % PEG lipid.

14. The method of claim 12 , wherein the PEG lipid is selected from the group consisting of a PEG-modified phosphatidylethanolamine, a PEG-modified phosphatidic acid, a PEG-modified ceramide, a PEG-modified dialkylamine, a PEG-modified diacylglycerol, and a PEG-modified dialkylglycerol.

15. The method of claim 12 , wherein the PEG lipid is

1) a compound of Formula (PL-I):

or salts thereof, wherein:

R 3 is —OR O ;

R O is hydrogen, optionally substituted alkyl, or an oxygen protecting group;

r is an integer between 1 and 100, inclusive;

L 1 is optionally substituted C 1-10 alkylene, wherein at least one methylene of the optionally substituted C 1-10 alkylene is independently replaced with optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, O, N(R N ), S, C(O), C(O)N(R N ), NR N C(O), C(O)O, —OC(O), OC(O)O, OC(O)N(R N ), NR N C(O)O, or NR N C(O)N(R N );

D is a moiety obtained by click chemistry or a moiety cleavable under physiological conditions;

m is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

A is of the formula:

each instance of L 2 is independently a bond or optionally substituted C 1-6 alkylene, wherein one methylene unit of the optionally substituted C 1-6 alkylene is optionally replaced with O, —N(R N ), S, C(O), C(O)N(R N ), NR N C(O), C(O)O, OC(O), OC(O)O, OC(O)N(R N ), NR N C(O)O, or NR N C(O)N(R N );

each instance of R 2 is independently optionally substituted C 1-30 alkyl, optionally substituted C 1-30 alkenyl, or optionally substituted C 1-30 alkynyl; optionally wherein one or more methylene units of R 2 are independently replaced with optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, N(R N ), O, S, C(O), C(O)N(R N ), NR N C(O), NR N C(O)N(R N ), C(O)O, OC(O), —OC(O)O, OC(O)N(R N ), NR N C(O)O, C(O)S, SC(O), C(═NR N ), C(═NR N )N(R N ), —NR N C(═NR N ), NR N C(═NR N )N(R N ), C(S), C(S)N(R N ), NR N C(S), NR N C(S)N(R N ), S(O), —OS(O), S(O)O, OS(O)O, OS(O) 2 , S(O) 2 O, OS(O) 2 O, N(R N )S(O), S(O)N(R N ), —N(R N )S(O)N(R N ), OS(O)N(R N ), N(R N )S(O)O, S(O) 2 , N(R N )S(O) 2 , S(O) 2 N(R N ), —N(R N )S(O) 2 N(R N ), OS(O) 2 N(R N ), or N(R N )S(O) 2 O;

each instance of R N is independently hydrogen, optionally substituted alkyl, or a nitrogen protecting group;

Ring B is optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; and

p is 1 or 2;

2) a compound of Formula (PL-II):

or a salt thereof, wherein:

R 3 is —OR O ;

R O is hydrogen, optionally substituted alkyl or an oxygen protecting group;

r is an integer between 1 and 100;

R 5 is optionally substituted C 10-40 alkyl, optionally substituted C 10-40 alkenyl, or optionally substituted C 10-40 alkynyl; and optionally one or more methylene groups of R 5 are replaced with optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, optionally substituted heteroarylene, N(R N ), O, S, C(O), C(O)N(R N ), —NR N C(O), NR N C(O)N(R N ), C(O)O, OC(O), OC(O)O, OC(O)N(R N ), NR N C(O)O, C(O)S, —SC(O), C(═NR N ), C(═NR N )N(R N ), NR N C(═NR N ), NR N C(═NR N )N(R N ), C(S), C(S)N(R N ), —NR N C(S), NR N C(S)N(R N ), S(O), OS(O), S(O)O, OS(O)O, OS(O) 2 , S(O) 2 O, OS(O) 2 O, —N(R N )S(O), S(O)N(R N ), N(R N )S(O)N(R N ), OS(O)N(R N ), N(R N )S(O)O, S(O) 2 , N(R N )S(O) 2 , —S(O) 2 N(R N ), N(R N )S(O) 2 N(R N ), OS(O) 2 N(R N ), or N(R N )S(O) 2 O; and

each instance of R N is independently hydrogen, optionally substituted alkyl, or a nitrogen protecting group;

3) a compound of Formula (PL-III):

or a salt or isomer thereof, wherein s is an integer between 1 and 100; or

4) a compound of Formula (PL-IV):

or salts thereof, wherein:

R 6 is C 1 -C 20 alkyl;

r is an integer between 0 and 100, inclusive;

R 6 is C 16 alkyl;

R 6 is C 18 alkyl.

16. The method of claim 12 , wherein the structural lipid is selected from the group consisting of cholesterol, fecosterol, sitosterol, ergosterol, campesterol, stigmasterol, brassicasterol, tomatidine, ursolic acid, and alpha-tocopherol.

17. The method of claim 12 , wherein the phospholipid is selected from the group consisting of 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-di-O-octadecenyl-sn-glycero-3-phosphocholine (18:0 Diether PC), 1-oleoyl-2-cholesterylhemisuccinoyl-sn-glycero-3-phosphocholine (OChemsPC), 1-hexadecyl-sn-glycero-3-phosphocholine (C16 Lyso PC), 1,2-dilinolenoyl-sn-glycero-3-phosphocholine, 1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-diphytanoyl-sn-glycero-3-phosphoethanolamine (ME 16.0 PE), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine, 1,2-dilinoleoyl-sn-glycero-3-phosphoethanolamine, 1,2-dilinolenoyl-sn-glycero-3-phosphoethanolamine, 1,2-diarachidonoyl-sn-glycero-3-phosphoethanolamine, 1,2-didocosahexaenoyl-sn-glycero-3-phosphoethanolamine, 1,2-dioleoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DOPG), and sphingomyelin.

18. The method of claim 1 , wherein the ionizable lipid is

1) a compound of Formula (IL-I):

or a salt thereof, wherein:

R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR″, —YR″, and —R″M′R′

R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;

R 4 is selected from the group consisting of hydrogen, a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from the group consisting of a carbocycle, heterocycle, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —N(R) 2 , —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —N(R)R 8 , N(R)S(O) 2 R 8 , —O(CH 2 ) n OR, —N(R)C(═NR 9 )N(R) 2 , —N(R)C(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, —N(OR)C(O)R, —N(OR)S(O) 2 R, —N(OR)C(O)OR, —N(OR)C(O)N(R) 2 , —N(OR)C(S)N(R) 2 , —N(OR)C(═NR 9 )N(R) 2 , —N(OR)C(═CHR 9 )N(R) 2 , —C(═NR 9 )N(R) 2 , —C(═NR 9 )R, —C(O)N(R)OR, and —C(R)N(R) 2 C(O)OR, and

each n is independently selected from the group consisting of 1, 2, 3, 4, and 5;

each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;

each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;

M and M′ are independently selected from the group consisting of —C(O)O—, —OC(O)—, —OC(O)-M″-C(O)O—,

—C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group, in which M″ is a bond, C 1-13 alkyl or C 2-13 alkenyl;

R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;

R 8 is selected from the group consisting of C 3-6 carbocycle and heterocycle;

R 9 is selected from the group consisting of H, CN, NO 2 , C 1-6 alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6 alkenyl, C 3-6 carbocycle and heterocycle;

each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;

each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR″, —YR″, and H;

each R″ is independently selected from the group consisting of C 3-15 alkyl and C 3-15 alkenyl;

each R* is independently selected from the group consisting of C 1-12 alkyl and C 2-12 alkenyl;

each Y is independently a C 3-6 carbocycle;

each X is independently selected from the group consisting of F, Cl, Br, and I; and

m is selected from the group consisting of 5, 6, 7, 8, 9, 10, 11, 12, and 13;

and wherein when R 4 is —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, or —CQ(R) 2 , then (i) Q is not —N(R) 2 when n is 1, 2, 3, 4 or 5, or (ii) Q is not 5, 6, or 7-membered heterocycloalkyl when n is 1 or 2;

2) a compound of Formula (IL-II):

or a salt thereof, wherein

l is selected from the group consisting of 1, 2, 3, 4 and 5;

M1 is a bond or M′;

R 4 is hydrogen, unsubstituted C 1-3 alkyl, or —(CH 2 ) n Q, in which n is 2, 3, or 4,

Q is —OH, —NHC(S)N(R) 2 , —NHC(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)R 8 , —NHC(═NR 9 )N(R) 2 , —NHC(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, heteroaryl or heterocycloalkyl;

M and M′ are independently selected from the group consisting of —C(O)O—, —OC(O)—, —OC(O)-M″-C(O)O—, —C(O)N(R′)—, —P(O)(OR′)O—, —S—S—, an aryl group, and a heteroaryl group; and

R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, and C 2-14 alkenyl; or

3) a compound of formula (IL-III):

or a salt thereof, wherein,

W is

ring A is

t is 1 or 2;

A 1 and A 2 are each independently selected from the group consisting of CH and N;

Z is CH 2 or absent wherein when Z is CH 2 , the dashed lines (1) and (2) each represent a single bond; and when Z is absent, the dashed lines (1) and (2) are both absent;

R 1 , R 2 , R 3 , R 4 , and R 5 are independently selected from the group consisting of C 5-20 alkyl, C 5-20 alkenyl, —R″MR′, —R*YR″, —YR″, and —R*OR″;

R X1 and R X2 are each independently H or C 1-3 alkyl;

each M is independently selected from the group consisting of —C(O)O—, —OC(O)—, —OC(O)O—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —C(O)S—, —SC(O)—, an aryl group, and a heteroaryl group;

M* is C 1 -C 6 alkyl,

W 1 and W 2 are each independently selected from the group consisting of —O— and —N(R 6 )—;

each R 6 is independently selected from the group consisting of H and C 1-5 alkyl;

X 1 , X 2 , and X 3 are independently selected from the group consisting of a bond, —CH 2 —, —(CH 2 ) 2 —, —CHR—, —CHY—, —C(O)—, —C(O)O—, —OC(O)—, —(CH 2 ) n —C(O)—, —C(O)—(CH 2 ) n —, —(CH 2 ) n —C(O)O—, —OC(O)—(CH 2 ) n —, —(CH 2 ) n —OC(O)—, —C(O)O—(CH 2 ) n —, —CH(OH)—, —C(S)—, and —CH(SH)—;

each Y is independently a C 3-6 carbocycle;

each R* is independently selected from the group consisting of C 1-12 alkyl and C 2-12 alkenyl;

each R is independently selected from the group consisting of C 1-3 alkyl and a C 3-6 carbocycle;

each R′ is independently selected from the group consisting of C 1-12 alkyl, C 2-12 alkenyl, and H;

each R″ is independently selected from the group consisting of C 3-12 alkyl, C 3-12 alkenyl and —R*MR′; and

n is an integer from 1-6,

wherein when ring A is

 then

i) at least one of X 1 , X 2 , and X 3 is not —CH 2 —; and/or

ii) at least one of R 1 , R 2 , R 3 , R 4 , and R 5 is —R″MR′.

19. The method of claim 1 , wherein the LNP formulation and/or LNP composition has a nitrogen:phosphorous (N:P) ratio from about 1:1 to about 30:1.