NZ719941B2 - Amino acid derivatives functionalized on the n-terminal capable of forming drug encapsulating microspheres - Google Patents

Abstract

Described herein are compounds and compositions that are characterized by the Markush formulae (I), (II), (III), (IV), (V), and (VI) underneath, where at least one terminal amino group is further functionalized by bearing a group of type (i), (ii), or (iii). Such compounds are obtained by reacting a terminal or internal amino group with epoxides, acrylates, or aldehydes bearing lipophilic groups. The resulting amino acid, peptide, polypeptide-lipids (named "APPLs" in the application) are deemed useful as drug delivery systems including nucleotide delivery to cells. terminal or internal amino group with epoxides, acrylates, or aldehydes bearing lipophilic groups. The resulting amino acid, peptide, polypeptide-lipids (named "APPLs" in the application) are deemed useful as drug delivery systems including nucleotide delivery to cells.

Description

AMINO ACID DERIVATIVES FUNCTIONALIZED ON THE N-TERMINAL CAPABLE OF FORMING DRUG ENCAPSULATING MICROSPHERES Related Applications The present application claims priority under 35 U.S.C. § 119(e) to U.S. provisional patent application, U.S.S.N. 61/552,423, filed October 27, 2011, which is incorporated herein by reference.

Government Support This invention was made with government t under Grant No. R37 EB000244 awarded by the National Institutes of Health. The government has certain rights in this invention.

Background of the Invention The y to e genes via RNA interference (RNAi) was ed by Mello and Fire in 1998. See Fire et al., Nature (1998) 391:806-811. Since then, scientists have rushed to take advantage of the enormous therapeutic potential driven by ed gene knockdown. This is ced by the fact that the first report of small interfering RNA (siRNA) mediated RNAi in human beings was reported only twelve years after the phenomenon was described in Caenorhabditis elegans. See Davis et al., Nature (2010) 464:1067-1070. It is well understood that development of c drugs is slowed by the inability to deliver nucleic acids effectively in vivo. When unprotected, genetic material injected into the bloodstream can be degraded by DNAases and RNAases, or, if not degraded, the genetic material can stimulate an immune response. See, e.g., Whitehead et al., Nature s Drug Discovery (2009) 8:129-138; Robbins et al., Oligonucleotides (2009) 19:89- 102. Intact siRNA must then enter the cytosol, where the antisense strand is incorporated into the RNA-induced silencing complex (RISC) (Whitehead supra). The RISC associates with and degrades complementary mRNA ces, thereby preventing ation of the target mRNA into protein, i.e., “silencing” the gene.

To overcome difficulties in delivery, nucleotides have been complexed with a wide variety of delivery systems, including polymers, lipids, inorganic nanoparticles and viruses. See, e.g., Peer et al. Nature Nanotechnology, (2007) 2:751-760. However, despite promising data from ongoing clinical trials for the treatment of respiratory syncytial virus and liver cancers (see, e.g., Zamora et al., Am. J. . Crit. Care Med. (2011) 183:531-538), WO 63468 the clinical use of siRNA continues to require development of safer and more effective delivery systems. Toward this end, numerous lipid—like molecules have been developed including poly o esters and amino alcohol lipids. See, e. 57., PCT Application Publication Nos. ; ; ; WO 43659; WC 2006/138380; and . Amino acid, peptide, polypeptide—lipids (APPL) have also been studied for a variety of applications, including use as therapeutics, biosurfactants, and tide delivery s. See, e. g., Giuliani et al., Cellular and Molecular Life Sciences (2011) 68:2255—2266; lkeda et al., Current Medicinal Chemistry (2007) 14: 111263-1275; Sen, es in Experimental Medicine and Biology (2010) 672:316-323; and Damen et al., Journal of Controlled Release (2010) 145:33—39. However, there continues to remain a need to investigate and develop new APPL systems with improved properties, such as new and ed APPL tide delivery systems.

Summary of the Invention Described herein are inventive compounds and compositions characterized, in certain embodiments, by conjugation of various groups, such as ilic groups, to an amino or amide group of an amino acid, a linear or cyclic peptide, a linear or cyclic polypeptide, or structural isomer thereof, to provide compounds of the present invention, collectively referred to herein as “APPLs”. Such APPLs are deemed useful for a variety of applications, such as, for example, improved nucleotide ry.

Exemplary APPLs include, but are not limited to, compounds of Formula (I), (II), (III), (IV), (V), and (VI), and salts thereof, as described herein: z R5 W F:3 1 R4 RZ—N m Y R1 R' R1 N RB’ RL R2\ Q R\ Q N NIN R1—< R1 R2‘ R1 Q R1 R2 Q (V) (VI) wherein m, n, p, R’, R1, R2, R3, R4, R5, R8, Z, W, Y, and Z are as defined , provided that the APPL comprises at least one instance of a group of formula (i), (ii), or (iii): E—Q\ RL RI g_/ 0) (ii) (iii) wherein: each instance of R’ is ndently hydrogen or ally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, ally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, n RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, ally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally substituted heteroC2_50 alkenyl, optionally substituted heteroC2_50 alkynyl, or a polymer.

In certain embodiments, the group of formula (i) represents a group of formula (i—a) or a group of formula (i—b): L | I R' RL (i-a) (i-b).

In certain embodiments, the group of formula (i—a) is a group of formula (i—al) or a group of formula : RL 8' Ra R' EfYRP ngRP RI RI (i-al) (i-a2).

In certain embodiments, the group of formula (i—b) is a group of formula (i—bl) or a group of formula (i—b2): R' IRL R' RL (i-bl) (i—b2) In certain ments, at least one instance of R1 is a group of formula: E—L—N R7 (iV) wherein L is an optionally substituted alkylene, optionally substituted lene, optionally substituted alkynylene, optionally tuted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, or optionally tuted heteroarylene, and R6 and R7 are independently selected from the group consisting of en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, and a nitrogen protecting group; provided at least one instance of R6 and R7 is a group of formula: . R‘ XRL RQ—YRP g—<R- § 0 R'- R' or §_/ (1) (ii) (iii) wherein: each instance of R’ is independently hydrogen or optionally tuted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, ally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally substituted heteroaryl, an oxygen ting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, ally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally tuted heteroC2_50 alkenyl, optionally substituted heteroC2_50 alkynyl, or a polymer.

In certain embodiments, each instance of R’ is hydrogen.

In certain embodiments, L is an optionally substituted alkylene.

In certain embodiments, the group of formula (iv) is of formula: “WNW wherein q is an integer between 1 and 50, inclusive.

In certain embodiments, each instance of R1 is a group of formula (iv).

An exemplary APPL of the present invention is compound (cKK-E12): 2012/062222 C10H21/S HO/[\/N 0 C10H21 C10H21 C10H21 H0 (cKK-E12), or a salt thereof.

In another aspect, provided are compositions comprising an APPL or a salt thereof.

For example, in certain embodiments, provided is a composition comprising an APPL or salt thereof and, optionally, an excipient, wherein the APPL is an amino acid, a linear or cyclic peptide, a linear or cyclic polypeptide, or structural isomer thereof, and wherein an amino or amide group of the APPL is ated to a group of formula (i), (ii), or (iii). In certain embodiments, the group of formula (i), (ii), or (iii) is attached to an amino group present on the APPL scaffold. In certain embodiments, the composition is a pharmaceutical composition, a cosmetic composition, a nutraceutical composition, or a composition with non—medical application. In certain embodiments, the composition with non—medical application is an emulsion or emulsifier useful as a food component, for extinguishing fires, for disinfecting surfaces, or for oil cleanup.

In certain embodiments, the composition further comprises an agent. In certain embodiments, the agent is an c molecule, inorganic molecule, nucleic acid, protein, peptide, cleotide, targeting agent, an isotopically labeled chemical compound, vaccine, an immunological agent, or an agent useful bioprocessing, e.g., in the intracellular manufacturing of proteins. In n embodiments, the agent is a polynucleotide, and the cleotide is DNA or RNA. In certain embodiments, the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA. In n embodiments, the agent and the APPL are not covalently ed, e.g., for example, the agent and the APPL are non—covalently complexed to each other. r, in n embodiments, the agent and the APPL are covalently attached.

WO 63468 In certain embodiments, the composition is in the form of a particle. In certain embodiments, the particle is a nanoparticle or microparticle. In certain embodiments, the particle is a micelle, liposome, or lipoplex. In certain embodiments, the le encapsulates an agent, 6.57., an agent to be red.

In another aspect, provided is a method of delivering a polynucleotide to a biological cell, comprising providing a composition comprising an APPL, or salt thereof, and a polynucleotide, and exposing the composition to the biological cell under conditions sufficient to facilitate delivery of the polynucleotide into the interior of the biological cell; wherein the APPL is an amino acid, a linear or cyclic peptide, or a linear or cyclic polypeptide, or structural isomer thereof, wherein an amino or amide group of the APPL is conjugated to a group of formula (i), (ii), or (iii). In certain ments, the polynucleotide is DNA or RNA. In certain embodiments, the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA. In certain embodiments, upon ry of the RNA into the cell, the RNA is able to interfere with the expression of a ic gene in the biological cell.

In yet another aspect, provided are screening methods. For example, in one embodiment, provided is a method of screening a compound library, the method comprising providing a plurality of different APPLs, or salts thereof, and performing at least one assay with the compound library to determine the presense or absence of a desired property; wherein the APPL is an amino acid, a linear or cyclic peptide, or a linear or cyclic polypeptide, or structural isomer f, wherein an amino or amide group of the APPL is conjugated to a group of formula (i), (ii), or (iii). In certain embodiments, the desired property is solubility in water, solubility at different pH, y to bind cleotides, ability to bind heparin, ability to bind small molecules, ability to bind protein, ability to form microparticles, ability to increase tranfection efficiency, ability to support cell growth, ability to support cell ment, ability to support tissue growth, and/or intracellular delivery of the APPL and/or an agent complexed or attached thereto to aid in bioprocessing.

In still yet another aspect, provided are methods of use of the inventive APPLs for the treatment of various diseases, disorders, or conditions. For example, in n ments, provided is a method of treating a disease, disorder, or condition from which the t suffers, sing administering to a subject in need thereof an effective amount of an APPL, or salt thereof, wherein the APPL is an amino acid, a linear or cyclic peptide, or a linear or cyclic polypeptide, or structural isomer thereof, n an amino or amide group of the APPL is ated to a group of formula (i), (ii), or (iii).

The details of one or more embodiments of the invention are set forth herein.

Other features, objects, and advantages of the invention will be apparent from the Detailed Description, the Figures, the Examples, and the Claims.

Definitions Chemical definitions Definitions of specific functional groups and chemical terms are bed in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., inside cover, and specific functional groups are generally defined as described n.

Additionally, general principles of organic chemistry, as well as specific onal moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito, 1999; Smith and March March’s Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive c Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern s of Organic Synthesis, 3rd n, Cambridge University Press, Cambridge, 1987.

Compounds described herein can se one or more asymmetric centers, and thus can exist in s isomeric forms, e. g., enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more isomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, ing chiral high pressure liquid chromatography (HPLC) and the formation and llization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, E.L. Stereochemistry of Carbon Compounds (McGraw—Hill, NY, 1962); and Wilen, S.H. Tables ofResolving Agents and Optical Resolutions p. 268 (EL. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, IN 1972). The ion additionally encompasses compounds as individual isomers substantially free of other isomers, and alternatively, as mixtures of s isomers.

When a range of values is listed, it is intended to encompass each value and sub—range within the range. For example “C14 alkyl” is intended to encompass, C1, C2, C3, C4, C5, C6, C176, C15, C14, C173, C172, C24, C25, C24, C273, C376, C375, C34, C46, C45, and C54 alkyl.

As used herein, “alkyl” refers to a radical of a straight—chain or branched saturated arbon group having from 1 to 50 carbon atoms (“C150 alkyl”). In some embodiments, an alkyl group has 1 to 40 carbon atoms (“C140 alkyl”). In some embodiments, an alkyl group has 1 to 30 carbon atoms (“C130 alkyl”). In some embodiments, an alkyl group has 1 to 20 carbon atoms (“C140 ). In some embodiments, an alkyl group has 1 to 10 carbon atoms (“C140 alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C19 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C1,g alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C14 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C14 alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“CH alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C14 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“CH alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“CH alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C1 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C2,6 alkyl”).

Examples of C14 alkyl groups include methyl (C1), ethyl (C2), n—propyl (C3), isopropyl (C3), n—butyl (C4), tert—butyl (C4), sec—butyl (C4), tyl (C4), n—pentyl (C5), 3—pentanyl (C5), amyl (C5), neopentyl (C5), 3—methyl—2—butanyl (C5), ry amyl (C5), and n—hexyl (C6).

Additional examples of alkyl groups include n—heptyl (C7), l (C8) and the like. Unless otherwise ied, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a ituted alkyl”) with one or more substituents. In certain ments, the alkyl group is an unsubstituted C150 alkyl. In certain embodiments, the alkyl group is a substituted C150 alkyl.

As used herein, “heteroalkyl” refers to an alkyl group as defined herein which further includes at least one heteroatom (e.g., l to 25, e.g., l, 2, 3, or 4 heteroatoms) selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus within (i.e., inserted n adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkyl group refers to a ted group haVing from 1 to 50 carbon atoms and l or more heteroatoms within the parent chain (“heteroCHo alkyl”).

In certain embodiments, a heteroalkyl group refers to a saturated group haVing from 1 to 40 carbon atoms and l or more heteroatoms within the parent chain (“heteroCHO alkyl”). In certain embodiments, a heteroalkyl group refers to a ted group haVing from 1 to 30 carbon atoms and l or more heteroatoms within the parent chain (“heteroCHo alkyl”). In certain embodiments, a heteroalkyl group refers to a saturated group haVing from 1 to 20 carbon atoms and l or more heteroatoms within the parent chain (“heteroCHO alkyl”). In certain ments, a heteroalkyl group refers to a saturated group having from 1 to 10 carbon atoms and l or more heteroatoms Within the parent chain (“heteroCHo alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 9 carbon atoms and l or more heteroatoms Within the parent chain (“heteroC1,9 alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 8 carbon atoms and l or more heteroatoms Within the parent chain (“heteroCHg alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 7 carbon atoms and l or more heteroatoms Within the parent chain (“heteroCH alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 6 carbon atoms and l or more heteroatoms Within the parent chain (“heteroCM alkyl”). In some embodiments, a heteroalkyl group is a ted group having 1 to 5 carbon atoms and l or 2 heteroatoms Within the parent chain roC1,5 alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and lor 2 atoms Within the parent chain (“heteroCH alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 3 carbon atoms and l heteroatom Within the parent chain (“heteroC1,3 alkyl”). In some embodiments, a alkyl group is a saturated group having 1 to 2 carbon atoms and l heteroatom Within the parent chain roCH alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 carbon atom and l heteroatom (“heteroC1 alkyl”). In some ments, a heteroalkyl group is a saturated group haVing 2 to 6 carbon atoms and l or 2 heteroatoms Within the parent chain (“heteroC2,6 alkyl”). Unless otherwise specified, each instance of a heteroalkyl group is independently unsubstituted (an “unsubstituted heteroalkyl”) or substituted (a “substituted heteroalkyl”) with one or more tuents. In certain embodiments, the heteroalkyl group is an unsubstituted heteroC1,50 alkyl. In certain embodiments, the alkyl group is a substituted C1,50 alkyl.

As used herein, “alkenyl” refers to a radical of a straight—chain or branched hydrocarbon group haVing from 2 to 50 carbon atoms and one or more carbon—carbon double bonds (e.g., l, 2, 3, or 4 double bonds) (“C250 alkenyl”). In some embodiments, an l group has 2 to 40 carbon atoms (“C240 alkenyl”). In some embodiments, an alkenyl group has 2 to 30 carbon atoms (“C230 alkenyl”). In some embodiments, an alkenyl group has 2 to carbon atoms (“C240 alkenyl”). In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C240 alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C2,9 alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C24, alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C24 alkeny ”). In some embodiments, an alkenyl group has 2 to 6 carbon atoms (“ng alkenyl”).

In some embodiments, an alkenyl group has 2 to 5 carbon atoms (“C2,5 alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (“C24 alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“CH l”). In some embodiments, an alkenyl group has 2 carbon atoms (“C2 alkenyl”). The one or more carbon—carbon double bonds can be internal (such as in nyl) or terminal (such as in l— butenyl). Examples of C24 alkenyl groups include ethenyl (C2), l—propenyl (C3), 2—propenyl (C3), l—butenyl (C4), nyl (C4), enyl (C4), and the like. Examples of C24 alkenyl groups e the aforementioned C24 alkenyl groups as well as pentenyl (C5), pentadienyl (C5), hexenyl (C6), and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (C3), octatrienyl (C3), and the like. Unless otherwise specified, each instance of an alkenyl group is independently unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more tuents. In certain embodiments, the alkenyl group is an unsubstituted C240 alkenyl. In certain ments, the alkenyl group is a substituted C240 alkenyl.

As used herein, “heteroalkenyl” refers to an l group as defined herein which further includes at least one heteroatom (e.g., l to 25, e.g., l, 2, 3, or 4 heteroatoms) selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In n embodiments, a heteroalkenyl group refers to a group haVing from 2 to 50 carbon atoms, at least one double bond, and l or more heteroatoms within the parent chain (“heteroC2,50 alkenyl”). In n embodiments, a heteroalkenyl group refers to a group haVing from 2 to 40 carbon atoms, at least one double bond, and l or more heteroatoms within the parent chain (“heteroC240 l”). In certain embodiments, a heteroalkenyl group refers to a group haVing from 2 to 30 carbon atoms, at least one double bond, and l or more heteroatoms within the parent chain (“heteroCHo alkenyl”). In certain embodiments, a heteroalkenyl group refers to a group haVing from 2 to 20 carbon atoms, at least one double bond, and l or more heteroatoms within the parent chain (“heteroC2,20 alkenyl”). In certain embodiments, a heteroalkenyl group refers to a group haVing from 2 to 10 carbon atoms, at least one double bond, and l or more heteroatoms within the parent chain (“heteroCHo alkeny ”). In some embodiments, a heteroalkenyl group has 2 to 9 carbon atoms at least one double bond, and l or more heteroatoms within the parent chain (“heteroC2,9 alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 8 carbon atoms, at least one double bond, and l or more heteroatoms within the parent chain (“heteroCHg alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 7 carbon atoms, at least one double bond, and l or more heteroatoms Within the parent chain (“heteroCzq alkenyl”). In some ments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and l or more heteroatoms Within the parent chain (“heteroC2,6 alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 5 carbon atoms, at least one double bond, and l or 2 heteroatoms Within the parent chain (“heteroC2,5 alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 4 carbon atoms, at least one double bond, and lor 2 heteroatoms Within the parent chain (“heteroC24 alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 3 carbon atoms, at least one double bond, and l heteroatom Within the parent chain (“heteroCH alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and l or 2 heteroatoms Within the parent chain (“heteroC2,6 alkeny ”). Unless otherwise ied, each ce of a heteroalkenyl group is ndently tituted (an “unsubstituted heteroalkenyl”) or substituted (a “substituted heteroalkenyl”) with one or more substituents. In certain embodiments, the heteroalkenyl group is an unsubstituted heteroC2,50 alkenyl. In certain embodiments, the heteroalkenyl group is a tuted heteroC2,50 alkenyl.

As used herein, “alkynyl” refers to a radical of a straight—chain or ed hydrocarbon group haVing from 2 to 50 carbon atoms and one or more carbon—carbon triple bonds (e.g., l, 2, 3, or 4 triple bonds) and optionally one or more double bonds (e.g., l, 2, 3, or 4 double bonds) (“C250 alkynyl”). An alkynyl group that has one or more triple bonds and one or more double bonds is also referred to as an ene”. In some embodiments, an alkynyl group has 2 to 40 carbon atoms (“C240 alkynyl”). In some embodiments, an alkynyl group has 2 to 30 carbon atoms (“C230 alkynyl”). In some embodiments, an l group has 2 to 20 carbon atoms (“C240 alkynyl”). In some embodiments, an alkynyl group has 2 to carbon atoms (“C240 alkynyl”). In some embodiments, an alkynyl group has 2 to 9 carbon atoms (“C2,9 alkynyl”). In some embodiments, an l group has 2 to 8 carbon atoms (“C24, alkynyl”). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (“C24 alkynyl”). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C24 alkynyl”).

In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C2,5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C24 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“CH alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C2 alkynyl”). The one or more carbon— carbon triple bonds can be internal (such as in 2—butynyl) or terminal (such as in l—butynyl).

Examples of C24 l groups include, Without limitation, ethynyl (C2), l—propynyl (C3), 2—propynyl (C3), l—butynyl (C4), 2—butynyl (C4), and the like. Examples of C24 alkenyl WO 63468 groups include the aforementioned C24 alkynyl groups as well as pentynyl (C5), hexynyl (C6), and the like. Additional examples of alkynyl include heptynyl (C7), octynyl (C3), and the like. Unless otherwise specified, each instance of an alkynyl group is independently unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents. In certain embodiments, the alkynyl group is an unsubstituted C250 alkynyl. In certain embodiments, the alkynyl group is a substituted C250 l.

As used herein, “heteroalkynyl” refers to an alkynyl group as defined herein which further includes at least one heteroatom (e.g., l to 25, e.g., l, 2, 3, or 4 heteroatoms) selected from , , nitrogen, boron, silicon, or phosphorus within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkynyl group refers to a group haVing from 2 to 50 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain (“heteroC2,50 alkynyl”). In certain embodiments, a heteroalkynyl group refers to a group haVing from 2 to 40 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain (“heteroC240 alkynyl”). In certain embodiments, a heteroalkynyl group refers to a group haVing from 2 to 30 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain roCHo alkynyl”). In certain embodiments, a alkynyl group refers to a group haVing from 2 to 20 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain (“heteroC2,20 alkynyl”). In certain embodiments, a heteroalkynyl group refers to a group haVing from 2 to 10 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain roCHo l”). In some embodiments, a heteroalkynyl group has 2 to 9 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain (“heteroC2,9 alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain (“heteroCHg alkynyl”). In some ments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and l or more atoms within the parent chain (“heterngq alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and l or more heteroatoms within the parent chain (“heteroC2,6 alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 5 carbon atoms, at least one triple bond, and l or 2 heteroatoms within the parent chain (“heteroC2,5 alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and lor 2 heteroatoms within the parent chain (“heteroC24 alkynyl”). In some embodiments, a alkynyl group has 2 to 3 carbon atoms, at least one triple bond, and l heteroatom within the parent chain (“heteroCH alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and l or 2 heteroatoms within the parent chain (“heteroC2,6 alkynyl”). Unless otherwise ied, each instance of a alkynyl group is independently unsubstituted (an “unsubstituted heteroalkynyl”) or substituted (a “substituted heteroalkynyl”) with one or more tuents. In certain embodiments, the heteroalkynyl group is an unsubstituted heteroC2,50 alkynyl. In certain embodiments, the heteroalkynyl group is a substituted heteroC2,50 alkynyl.

As used herein, “carbocyclyl” or “carbocyclic” refers to a radical of a non— aromatic cyclic hydrocarbon group haVing from 3 to 10 ring carbon atoms (“C340 carbocycly ”) and zero heteroatoms in the non—aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms (“C3,g carbocyclyl”). In some ments, a carbocyclyl group has 3 to 7 ring carbon atoms (“C34 carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C34 carbocyclyl”). In some embodiments, a carbocyclyl group has 4 to 6 ring carbon atoms (“C44 carbocyclyl”). In some embodiments, a yclyl group has 5 to 6 ring carbon atoms (“C54 carbocyclyl”). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms (“C540 carbocyclyl”).

Exemplary C34 carbocyclyl groups e, without tion, cyclopropyl (C3), cyclopropenyl (C3), utyl (C4), cyclobutenyl (C4), cyclopentyl (C5), cyclopentenyl (C5), cyclohexyl (C6), cyclohexenyl (C6), cyclohexadienyl (C6), and the like. Exemplary C34; yclyl groups include, t limitation, the aforementioned C34 carbocyclyl groups as well as cycloheptyl (C7), cycloheptenyl (C7), cycloheptadienyl (C7), cycloheptatrienyl (C7), ctyl (C3), cyclooctenyl (C3), bicyclo[2.2.l]heptanyl (C7), bicyclo[2.2.2]octanyl (C3), and the like. Exemplary C340 carbocyclyl groups include, without limitation, the aforementioned C34; carbocyclyl groups as well as cyclononyl (C9), cyclononenyl (C9), cyclodecyl (C10), cyclodecenyl (C10), octahydro—lH—indenyl (C9), decahydronaphthalenyl (C10), spiro[4.5]decanyl (C10), and the like. As the foregoing examples illustrate, in n embodiments, the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or polycyclic (e.g., containing a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) or tricyclic system (“tricyclic carbocyclyl”)) and can be saturated or can contain one or more carbon—carbon double or triple bonds. “Carbocyclyl” also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups n the point of attachment is on the carbocyclyl ring, and in such ces, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is 2012/062222 independently unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents. In n embodiments, the carbocyclyl group is an unsubstituted C340 carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C340 carbocyclyl.

In some embodiments, “carbocyclyl” or “carbocyclic” is referred to as a “cycloalkyl”, i.e., a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C340 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C3,g cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C34 cycloalkyl”). In some embodiments, a cycloalkyl group has 4 to 6 ring carbon atoms (“C44 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C54 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C540 lkyl”). Examples of C54 cycloalkyl groups include entyl (C5) and cyclohexyl (C5). Examples of C3,6 cycloalkyl groups include the aforementioned C5,6 cycloalkyl groups as well as cyclopropyl (C3) and cyclobutyl (C4). Examples of C34; cycloalkyl groups include the aforementioned C34 cycloalkyl groups as well as cycloheptyl (C7) and cyclooctyl (C3). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents. In certain embodiments, the lkyl group is an tituted C340 cycloalkyl. In certain embodiments, the cycloalkyl group is a tuted C340 cycloalkyl.

As used herein, “heterocyclyl” or “heterocyclic” refers to a radical of a 3— to l4—membered omatic ring system having ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms, wherein each heteroatom is independently selected from , sulfur, nitrogen, boron, silicon, or phosphorus (“3—14 membered heterocyclyl”). In heterocyclyl groups that n one or more en atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”) or tricyclic system (“tricyclic cyclyl”)), and can be saturated or can contain one or more carbon—carbon double or triple bonds.

Heterocyclyl polycyclic ring systems can include one or more atoms in one or both rings. “Heterocyclyl” also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or cyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of WO 63468 attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless ise specified, each instance of heterocyclyl is independently unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents. In certain embodiments, the heterocyclyl group is an unsubstituted 3—l4 membered heterocyclyl. In n embodiments, the heterocyclyl group is a substituted 3—l4 ed heterocyclyl.

In some embodiments, a cyclyl group is a 5—10 membered non—aromatic ring system haVing ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms, wherein each heteroatom is independently selected from oxygen, , nitrogen, boron, silicon, or phosphorus (“5—10 ed heterocyclyl”). In some embodiments, a heterocyclyl group is a 5—8 membered non—aromatic ring system haVing ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms, wherein each heteroatom is independently selected from oxygen, sulfur, en, boron, silicon, or phosphorus (“5—8 membered heterocyclyl”). In some ments, a heterocyclyl group is a 5—6 membered non—aromatic ring system haVing ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms, wherein each heteroatom is independently selected from oxygen, , nitrogen, boron, silicon, or phosphorus (“5—6 membered heterocyclyl”). In some embodiments, the 5—6 membered heterocyclyl has 1 or more (e.g., l, 2, or 3) ring heteroatoms selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus. In some embodiments, the 5—6 membered heterocyclyl has 1 or 2 ring heteroatoms selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus. In some embodiments, the 5—6 membered heterocyclyl has 1 ring heteroatom selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus.

Exemplary 3—membered heterocyclyl groups containing 1 atom include, without limitation, azirdinyl, oxiranyl, thiorenyl. Exemplary 4—membered heterocyclyl groups ning 1 heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5—membered heterocyclyl groups containing 1 heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, othiophenyl, pyrrolidinyl, dihydropyrrolyl and yl—2,5—dione. Exemplary 5— membered heterocyclyl groups containing 2 heteroatoms include, without limitation, anyl, oxathiolanyl and dithiolanyl. Exemplary 5—membered cyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, zolinyl, and thiadiazolinyl. Exemplary 6—membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, opyridinyl, and thianyl.

Exemplary 6—membered heterocyclyl groups containing 2 heteroatoms include, without limitation, piperazinyl, linyl, dithianyl, dioxanyl. ary 6—membered heterocyclyl groups ning 2 heteroatoms include, without limitation, triazinanyl.

Exemplary 7—membered heterocyclyl groups containing 1 heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8—membered heterocyclyl groups containing 1 heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.

Exemplary bicyclic heterocyclyl groups include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, obenzothienyl, tetrahydrobenzothienyl, ydrobenzofuranyl, ydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyl, decahydronaphthyridinyl, decahydro—l ,8—naphthyridinyl, octahydropyrrolo[3,2—b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyl, lH—benzo[e][l,4]diazepinyl, l,4,5,7—tetrahydropyrano[3,4—b]pyrrolyl, 5,6—dihydro—4H—furo[3,2—b]pyrrolyl, 6,7—dihydro— 5H—furo[3,2—b]pyranyl, 5,7—dihydro—4H—thieno[2,3—c]pyranyl, hydro—lH— pyrrolo[2,3—b]pyridinyl, 2,3—dihydrofuro[2,3—b]pyridinyl, 4,5,6,7—tetrahydro—lH—pyrrolo— [2,3—b]pyridinyl, 4,5,6,7—tetrahydrofuro[3,2—c]pyridinyl, 4,5,6,7—tetrahydrothieno[3,2— dinyl, l,2,3,4—tetrahydro—l,6—naphthyridinyl, and the like.

As used herein, “aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., haVing 6, 10, or 14 at electrons shared in a cyclic array) haVing 6—l4 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C644 aryl”). In some embodiments, an aryl group has 6 ring carbon atoms (“C6 aryl”; e.g., phenyl). In some ments, an aryl group has 10 ring carbon atoms (“C10 aryl”; e.g., naphthyl such as l—naphthyl and 2—naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms (“C14 aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each ce of an aryl group is independently tituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents. In certain embodiments, the aryl group is an unsubstituted C644 aryl. In certain embodiments, the aryl group is a tuted C644 aryl.

As used , “heteroaryl” refers to a radical of a 5—14 membered monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., haVing 6, 10, or 14 at electrons shared in a cyclic array) having ring carbon atoms and l or more (e.g., l, 2, 3, or 4 ring heteroatoms) ring heteroatoms provided in the aromatic ring , wherein each heteroatom is independently selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus (“5—14 membered heteroaryl”). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits.

Heteroaryl clic ring systems can e one or more heteroatoms in one or both rings.

“Heteroaryl” includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of ment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring . Polycyclic heteroaryl groups wherein one ring does not contain a atom (e.g., indolyl, quinolinyl, olyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2—indolyl) or the ring that does not contain a heteroatom (e.g., 5—indolyl).

In some embodiments, a heteroaryl group is a 5—10 ed aromatic ring system having ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is ndently selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus (“5—10 membered heteroaryl”). In some ments, a heteroaryl group is a 5—8 membered aromatic ring system having ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms provided in the aromatic ring , wherein each heteroatom is ndently selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus (“5—8 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5—6 membered ic ring system having ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus (“5—6 membered heteroaryl”). In some embodiments, the 5—6 membered heteroaryl has 1 or more (e.g., l, 2, or 3) ring heteroatoms selected from oxygen, sulfur, en, boron, silicon, or phosphorus. In some embodiments, the 5—6 membered heteroaryl has 1 or 2 ring atoms selected from oxygen, , nitrogen, boron, silicon, or phosphorus. In some embodiments, the 5—6 membered heteroaryl has 1 ring heteroatom selected from oxygen, sulfur, nitrogen, boron, silicon, or orus. Unless otherwise specified, each instance of a heteroaryl group is independently unsubstituted (an “unsubstituted heteroaryl”) or tuted (a “substituted aryl”) with one or more substituents. In certain ments, the aryl group is an unsubstituted 5—14 membered heteroaryl. In certain embodiments, the heteroaryl group is a substituted 5—14 membered heteroaryl.

Exemplary 5—membered heteroaryl groups containing 1 heteroatom include, Without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary 5—membered heteroaryl groups containing 2 atoms include, Without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and azolyl. Exemplary 5—membered heteroaryl groups containing 3 heteroatoms include, Without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary —membered heteroaryl groups containing 4 heteroatoms include, Without limitation, tetrazolyl. Exemplary 6—membered heteroaryl groups containing 1 heteroatom include, Without limitation, pyridinyl. Exemplary 6—membered heteroaryl groups containing 2 heteroatoms include, Without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. ary 6—membered heteroaryl groups containing 3 or 4 heteroatoms include, t limitation, triazinyl and tetrazinyl, tively. Exemplary 7—membered heteroaryl groups containing 1 heteroatom include, Without tion, azepinyl, oxepinyl, and thiepinyl. ary 5,6— bicyclic heteroaryl groups include, Without tion, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6—bicyclic heteroaryl groups include, Without tion, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, alinyl, phthalazinyl, and quinazolinyl. Exemplary lic heteroaryl groups include, Without limitation, phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.

As used , the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term “partially unsaturated” is intended to encompass rings haVing multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl moieties) as herein defined.

As used herein, the term “saturated” refers to a ring moiety that does not contain a double or triple bond, i.e., the ring contains all single bonds.

Affixing the suffix “—ene” to a group tes the group is a divalent moiety, e.g., alkylene is the divalent moiety of alkyl, alkenylene is the divalent moiety of alkenyl, WO 63468 alkynylene is the divalent moiety of alkynyl, heteroalkylene is the divalent moiety of heteroalkyl, heteroalkenylene is the divalent moiety of heteroalkenyl, heteroalkynylene is the divalent moiety of heteroalkynyl, carbocyclylene is the divalent moiety of carbocyclyl, heterocyclylene is the divalent moiety of heterocyclyl, arylene is the divalent moiety of aryl, and heteroarylene is the divalent moiety of heteroaryl.

As understood from the above, alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, are, in n embodiments, optionally substituted. Optionally substituted refers to a group which may be substituted or unsubstituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” heteroalkyl, “substituted” or “unsubstituted” heteroalkenyl, “substituted” or stituted” heteroalkynyl, “substituted” or stituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or stituted” heteroaryl group). In general, the term “substituted” means that at least one hydrogen present on a group is replaced with a sible substituent, e.g., a substituent which upon tution results in a stable nd, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless ise ted, a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each on. The term ituted” is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound. The present invention contemplates any and all such combinations in order to arrive at a stable nd. For es of this invention, atoms such as nitrogen may have hydrogen tuents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.

Exemplary carbon atom substituents e, but are not limited to, halogen, — CN, —N02, —N3, —SOZH, —SO3H, —OH, —0Raa, —ON(Rbb)2, —N(Rbb)2, —N(Rbb)3+X’, — N(OR°°)Rbb, -SeH, -SeRaa, —SH, —SRaa, —SSR°°, 41(=0)Raa, —C02H, —CHO, —C(OR°°)2, — cozRaa, —0C(=0)Raa, —ocozRaa, —C(=O)N(Rbb)2, —OC(=O)N(Rbb)2, —NRbbC(=O)Raa, — NRbbcozRaa, —NRbbC(=O)N(Rbb)2, —C(=NRbb)Raa, —C(=NRbb)ORaa, —OC(=NRbb)Raa, — OC(=NRbb)ORaa, —C(=NRbb)N(Rbb)2, —OC(=NRbb)N(Rbb)2, —NRbbC(=NRbb)N(Rbb)2, — C(=O)NRbbSOZRaa, —NRbb802Raa, —SOZN(Rbb)2, —sozRaa, 502011”, —osozRaa, Raa, —OS(=O)Raa, —Si(Raa)3, —OSi(Raa)3 —C(=S)N(Rbb)2, —C(=O)SRaa, —C(=S)SRaa, —SC(=S)SRaa, —SC(=O)SRaa, —OC(=O)SRaa, —SC(=O)ORaa, —SC(=O)Raa, —P(=O)2Raa, —OP(=O)2Raa, — P<=0><Raa>2, —0P<=0><Raa>2, —0P<=0><0R°°>2, —P<=0>2N<Rbb>2, —0P<=0>2N<Rbb>2, — P<=0><NRbb>2, —0P<=0><NR"">2, —NR""P<=0><0R°°>2, —NRbbP<=0><NRbb>2, —P<R°°>2, — P(R°°)3, —OP(R°°)2, —OP(R°°)3, —B(Raa)2, —B(OR°°)2, —BRaa(OR°°), C140 alkyl, C240 alkenyl, C240 alkynyl, C344 carbocyclyl, 3—l4 membered heterocyclyl, C644 aryl, and 5—14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, yclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups; or two geminal ens on a carbon atom are replaced with the group =0, :8, =NN(Rbb)2, =NNRbbC(=O)Raa, =NNRbbC(=O)ORaa, =NNRbbS(=O)2Raa, =NRbb, or =NOR°°; each ce of Raa is, independently, selected from C140 alkyl, C240 alkenyl, C250 l, C340 carbocyclyl, 3—l4 membered heterocyclyl, C644 aryl, and 5—14 membered heteroaryl, or two Raa groups are joined to form a 3—14 membered heterocyclyl or 5—14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, yclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups; each instance of Rbb is, independently, selected from hydrogen, —OH, —ORaa, — N(RC°)2, —CN, —C(=O)Raa, —C(=O)N(R°C)2, —C02Raa, —SOzRaa, °°)ORaa, — C(=NR°°)N(R°°)2, —SOZN(RCC)2, —SOZR°°, —SOZOR°°, —SORaa, —C(=S)N(R°°)2, —C(=O)SR°°, — RCC, —P(=O)2Raaa —P(=O)(Raa)2, 2N(RCC)2, —P(=O)(NRCC)2, C1750 alkyl, C2750 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—l4 membered heterocyclyl, C644 aryl, and 5—14 ed heteroaryl, or two Rbb groups are joined to form a 3—14 membered heterocyclyl or —14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups; each instance of RCC is, independently, selected from hydrogen, C150 alkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—l4 ed cyclyl, C644 aryl, and 5—14 membered heteroaryl, or two RCC groups are joined to form a 3—14 membered heterocyclyl or —14 ed heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups; each instance of Rdd is, independently, selected from halogen, —CN, —N02, —N3, — SOZH, —SO3H, —OH, —0Ree, —ON(Rff)2, —N(Rff)2, )3+X’, —N(ORee)Rff, —SH, —SRee, — SSRee, —C(=0)Ree, —C02H, —C02Ree, —0C(=0)Ree, —ocozRei N(Rff)2, — OC(=O)N(Rff)2, —NRffC(=O)Ree, —NRffCOZRee, —NRffC(=O)N(Rff)2, —C(=NRff)ORee, — OC(=NRff)Ree, Rff)ORee, —C(=NRff)N(Rff)2, —OC(=NRff)N(Rff)2, — NRffC(=NRff)N(Rff)2,—NRffSOzRee, —SOZN(Rff)2, —sozRee, 50201166, —osozRee, —S(=0)Ree, —Si(Ree)3, —OSi(Ree)3, —C(=S)N(Rff)2, —C(=O)SRee, —C(=S)SRee, —SC(=S)SRee, —P(=O)2Ree, — P(=O)(Ree)2, —OP(=O)(Ree)2, —OP(=O)(ORee)2, C140 alkyl, C250 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—10 ed heterocyclyl, C640 aryl, 5—10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rgg groups, or two geminal Rdd substituents can be joined to form =0 or :8; each instance of R66 is, independently, selected from C140 alkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, CMO aryl, 3—10 membered heterocyclyl, and 3—10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is ndently substituted with 0, l, 2, 3, 4, or 5 Rgg groups; each instance of Rff is, independently, selected from hydrogen, C140 alkyl, C240 alkenyl, C240 l, C340 carbocyclyl, 3—10 membered heterocyclyl, C640 aryl and 5—10 membered heteroaryl, or two Rff groups are joined to form a 3—14 ed heterocyclyl or —14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rgg groups; and each instance of Rgg is, independently, halogen, —CN, —N02, —N3, —SOZH, —SO3H, — OH, —OC1,50 alkyl, —ON(C1,50 alkyl)2, —N(C1,50 alkyl)2, —N(C1,50 alkyl)3+X’, —NH(C1,50 alkyl)2+X’, —NH2(C1,50 alkyl) +X’, —NH3+X’, —N(OC1,50 alkyl)(C1,50 alkyl), —N(OH)(C1,50 alkyl), —NH(OH), —SH, —SC1,50 alkyl, ,50 alkyl), —C(=O)(C1,50 alkyl), —C02H, — C02(C1,50 alkyl), —OC(=O)(C1,50 alkyl), C1,50 alkyl), —C(=O)NH2, —C(=O)N(C1,50 alkyl)2, —OC(=O)NH(C1,50 alkyl), —NHC(=O)( C140 alkyl), —N(C1,50 alkyl)C(=O)( C140 , —NHC02(C1,50 alkyl), —NHC(=O)N(C1,50 alkyl)2, —NHC(=O)NH(C1,50 alkyl), — )NH2, —C(=NH)O(C1,50 ,—OC(=NH)(C1,50 alkyl), —OC(=NH)OC1,50 alkyl, — C(=NH)N(C1,50 alkyl)2, —C(=NH)NH(C1,50 alkyl), —C(=NH)NH2, —OC(=NH)N(C1,50 alkyl)2, —OC(NH)NH(C1,50 alkyl), —OC(NH)NH2, —NHC(NH)N(C1,50 alkyl)2, — NHC(=NH)NH2, (C1,50 alkyl), —SOZN(C1,50 alkyl)2, —SOZNH(C1,50 alkyl), — SOZNH2,—SOZC1,50 alkyl, —SOZOC1,50 alkyl, —OSOZC14 alkyl, —SOC1,6 alkyl, —Si(C1,50 alkyl)3, —OSi(C14 3 —C(=S)N(C1,50 alkyl)2, C(=S)NH(C1,50 alkyl), H2, — C(=O)S(C1,6 alkyl), —C(=S)SC1,6 alkyl, —SC(=S)SC14 alkyl, —P(=O)2(C1,50 alkyl), — P(=O)(C1,50 alkyl)2, —OP(=O)(C1,50 alkyl)2, —OP(=O)(OC1,50 2, C150 alkyl, C240 l, C240 l, C340 carbocyclyl, C640 aryl, 3—10 membered heterocyclyl, 5—10 membered aryl; or two l Rgg substituents can be joined to form =0 or :8; wherein X’ is a counterion.

As used herein, the term “halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro, —Cl), bromine (bromo, —Br), or iodine (iodo, —I).

As used herein, a “counterion” is a negatively charged group associated with a positively charged quarternary amine in order to maintain electronic neutrality. Exemplary counterions include halide ions (e.g., F Cl Br I , , ), N03 OH , , C104 , , H2P04’, H8047, sulfonate ions (e.g., methansulfonate, romethanesulfonate, p—toluenesulfonate, benzenesulfonate, lO—camphor sulfonate, naphthalene—2—sulfonate, naphthalene—l—sulfonic acid—5—sulfonate, ethan—l—sulfonic acid—2—sulfonate, and the like), and carboxylate ions (e.g., acetate, ethanoate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, and the like).

Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and rnary nitrogen atoms. Exemplary nitrogen atom substitutents include, but are not limited to, hydrogen, —OH, —ORaa, —N(R°°)2, —CN, — C(=0)Raa, —C(=O)N(RCC)2, —C02Raa, —sozRaa, —C(=NRbb)Raa, —C(=NR°°)ORaa, — °)N(R°°)2, —SOzN(RCC)2, —SOgR°°, —SOgOR°°, —SORaa, —C(=S)N(RC°)2, SRC°, — C(=S)SRCC, —P(=O)2Raaa —P(=O)(Raa)2, —P(=O)2N(RCC)2, —P(=O)(NRCC)2, C1750 alkyl, C2750 alkenyl, C240 alkynyl, C340 yclyl, 3—14 membered heterocyclyl, C644 aryl, and 5—14 membered heteroaryl, or two RCC groups attached to an N atom are joined to form a 3—14 ed cyclyl or 5—14 membered heteroaryl ring, wherein each alkyl, l, alkynyl, carbocyclyl, heterocyclyl, aryl, and aryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups, and wherein R”, Rbb, RCC and Rdd are as defined above.

Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms. Exemplary en atom substitutents e, but are not limited to, hydrogen, —OH, —ORaa, —N(R°°)2, —CN, — C(=0)Raa, —C(=O)N(RCC)2, —C02Raa, a, —C(=NRbb)Raa, —C(=NR°°)ORaa, — C(=NR°°)N(R°°)2, —SOzN(RCC)2, —SOgR°°, —SOgOR°°, —SORaa, —C(=S)N(RC°)2, —C(=O)SRC°, — C(=S)SRC°, 2Raa, —P(=0)(Raa)2, —P(=O)2N(RC°)2, —P(=0)(NR°°)2, C1710 alkyl, C1710 perhaloalkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—14 ed heterocyclyl, C644 aryl, and 5—14 ed heteroaryl, or two RCC groups attached to a nitrogen atom are joined to form a 3—14 membered heterocyclyl or 5—14 membered heteroaryl ring, wherein each alkyl, alkenyl, l, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups, and wherein R”, Rbb, RCC and Rdd are as defined above.

In certain ments, the substituent t on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting . Nitrogen protecting groups include, but are not limited to, —OH, —ORaa, —N(R°°)2, —C(=O)Raa, —C(=O)N(R°C)2, —C02Raa, —SOgRaa, —C(=NR°°)Raa, —C(=NR°°)ORaa, —C(=NR°°)N(R°°)2, —SOzN(R°°)2, —SOgR°°, — SOZORCC, —SORaa, —C(=S)N(R°°)2, —C(=O)SR°°, —C(=S)SR°°, C140 alkyl (e.g., aralkyl, heteroaralkyl), C240 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—14 membered cyclyl, C644 aryl, and 5—14 membered heteroaryl groups, wherein each alkyl, alkenyl, l, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein R”, Rbb, RCC and Rdd are as defined herein. Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in c Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, orated herein by reference.

For example, nitrogen protecting groups such as amide groups (e.g., — C(=O)Raa) include, but are not d to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3—phenylpropanamide, picolinamide, 3—pyridylcarboxamide, N—benzoylphenylalanyl derivative, benzamide, p— phenylbenzamide, 0—nitophenylacetamide, ophenoxyacetamide, acetoacetamide, (N’— dithiobenzyloxyacylamino)acetamide, 3—(p—hydroxyphenyl)propanamide, 3—(0— nitrophenyl)propanamide, 2—methyl—2—(0—nitrophenoxy)propanamide, 2—methyl—2—(0— phenylazophenoxy)propanamide, 4—chlorobutanamide, 3—methyl—3—nitrobutanamide, 0— nitrocinnamide, N—acetylmethionine derivative, 0—nitrobenzamide and 0— (benzoyloxymethyl)benzamide.

Nitrogen protecting groups such as carbamate groups (e.g., —C(=O)ORaa) include, but are not limited to, methyl carbamate, ethyl ante, 9—fluorenylmethyl carbamate , 9—(2—sulfo)fluorenylmethyl carbamate, 9—(2,7—dibromo)fluoroenylmethyl carbamate, 2,7 di t butyl [9 (10,10 dioxo 10,10—tetrahydrothioxanthyl)]methyl carbamate (DBD—Tmoc), 4—methoxyphenacyl carbamate c), 2,2,2—trichloroethyl carbamate (Troc), 2—trimethylsilylethyl carbamate (Teoc), 2—phenylethyl carbamate (hZ), 1— (1—adamantyl)—1—methylethyl carbamate ), 1,1—dimethyl—2—haloethyl carbamate, 1,1—dimethyl—2,2—dibromoethyl carbamate (DB—t—BOC), 1,1—dimethyl—2,2,2—trichloroethyl carbamate (TCBOC), 1—methyl—1—(4—biphenylyl)ethyl carbamate (Bpoc), 1—(3,5—di—t— butylphenyl)—1—methylethyl carbamate (t—Bumeoc), 2—(2’— and 4’—pyridyl)ethyl carbamate (Pyoc), 2—(N,N—dicycloheXylcarboxamido)ethyl carbamate, t—butyl carbamate (BOC), 1— adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl ate (Alloc), 1— 2012/062222 pylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4—nitrocinnamy1 carbamate (Noe), 8—quinoly1 carbamate, N—hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p—methoxybenzyl ate (Moz), p—nitobenzyl carbamate, 1)— bromobenzyl carbamate, p—chlorobenzyl carbamate, 2,4—dichlorobenzy1 carbamate, 4— methylsulfinylbenzyl carbamate (Msz), 9—anthry1methy1 carbamate, diphenylmethyl carbamate, 2—methy1thioethy1 carbamate, 2—methy1sulfony1ethy1 carbamate, 2—(p— toluenesulfony1)ethy1 carbamate, 3—dithiany1)]methy1 carbamate , 4— thiophenyl ate (Mtpc), 2,4—dimethy1thiopheny1 carbamate (Bmpc), 2— phosphonioethyl ate (Peoc), 2—tripheny1phosphonioisopropyl carbamate (Ppoc), 1,1— dimethyl—Z—cyanoethyl carbamate, m—chloro—p—acyloxybenzyl carbamate, 1)— (dihydroxybory1)benzy1 carbamate, 5—benzisoxazolylmethy1 carbamate, 2—(trifluoromethy1)— 6—chromony1methy1 carbamate (Tcroc), m—nitrophenyl carbamate, 3,5—dimethoxybenzy1 carbamate, 0—nitrobenzy1 carbamate, 3,4—dimethoxy—6—nitrobenzy1 carbamate, pheny1(0— nitropheny1)methy1 ate, t—amyl carbamate, S—benzyl thiocarbamate, p—cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p—decyloxybenzyl carbamate, 2,2—dimethoxyacy1viny1 carbamate, —dimethylcarboxamido)benzy1 carbamate, 1,1—dimethy1—3—(N,N— dimethylcarboxamido)propy1 carbamate, 1,1—dimethy1propyny1 carbamate, di(2— pyridy1)methy1 carbamate, 2—furany1methy1 carbamate, 2—iodoethy1 carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p—(p’—methoxyphenylazo)benzy1 carbamate, 1—methy1cyclobuty1carbamate, 1—methy1cyclohexy1carbamate, 1—methy1—1— cyclopropylmethyl carbamate, 1—methy1—1—(3,5—dimethoxypheny1)ethy1 carbamate, 1— methyl—1—(p—pheny1azopheny1)ethy1 ate, 1—methy1—1—pheny1ethy1 carbamate, 1— —l—(4—pyridy1)ethy1 carbamate, phenyl ate, p—(phenylazo)benzy1 carbamate, tri—t—butylpheny1 carbamate, 4—(trimethy1ammonium)benzy1 carbamate, and 2,4,6— trimethylbenzyl carbamate.

Nitrogen protecting groups such as sulfonamide groups (e.g., —S(=O)2Raa) include, but are not limited to, p—toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,— trimethy1—4—methoxybenzenesulfonamide (Mtr), 2,4,6—trimethoxybenzenesulfonamide (Mtb), 2,6—dimethy1—4—methoxybenzenesulfonamide (Pme), 2,3,5,6—tetramethy1—4— methoxybenzenesulfonamide (Mte), 4—methoxybenzenesulfonamide (Mbs), 2,4,6— trimethylbenzenesulfonamide (Mts), 2,6—dimethoxy—4—methy1benzenesulfonamide (iMds), 2,2,5,7,8—pentamethylchroman—6—sulfonamide (Pmc), methanesulfonamide (Ms), B— trimethylsilylethanesulfonamide (SES), 9—anthracenesulfonamide, 4—(4’,8’— dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to, phenothiazinyl—(lO)—acyl derivative, oluenesulfonylaminoacyl derivative, N’— phenylaminothioacyl derivative, N—benzoylphenylalanyl derivative, N—acetylmethionine derivative, 4,5—diphenyl—3—oxazolin—2—one, N—phthalimide, N—dithiasuccinimide (Dts), N— 2,3—diphenylmaleimide, dimethylpyrrole, N—l , l ,4,4— ethyldisilylazacyclopentane adduct (STABASE), 5—substituted l,3—dimethyl—l,3,5— triazacyclohexan—2—one, 5—substituted l,3—dibenzyl—l,3,5—triazacyclohexan—2—one, l— substituted nitro—4—pyridone, N—methylamine, N—allylamine, N—[2— (trimethylsilyl)ethoxy]methylamine (SEM), N—3—acetoxypropylamine, N—(l—isopropyl—4— nitro—2—oxo—3—pyroolin—3—yl)amine, quaternary ammonium salts, N—benzylamine, N—di(4— methoxyphenyl)methylamine, N—S—dibenzosuberylamine, N—triphenylmethylamine (Tr), N— [(4—methoxyphenyl)diphenylmethyl]amine , N—9—phenylfluorenylamine (PhF), N— chloro—9—fluorenylmethyleneamine, N—ferrocenylmethylamino (ch), N—2— picolylamino N’—oxide, N—l,l—dimethylthiomethyleneamine, N—benzylideneamine, N—p— methoxybenzylideneamine, N—diphenylmethyleneamine, N—[(2— pyridyl)mesityl]methyleneamine, N—(N’,N’—dimethylaminomethylene)amine, N,N’— isopropylidenediamine, N—p—nitrobenzylideneamine, N—salicylideneamine, N—S— chlorosalicylideneamine, N—(5—chloro—2—hydroxyphenyl)phenylmethyleneamine, N— cyclohexylideneamine, N—(S,5—dimethyl—3—oxo—l—cyclohexenyl)amine, N—borane derivative, N—diphenylborinic acid derivative, N—[phenyl(pentaacylchromium— or tungsten)acyl]amine, N—copper chelate, N—zinc chelate, N—nitroamine, N—nitrosoamine, amine N—oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl oramidate, diphenyl phosphoramidate, benzenesulfenamide, 0—nitrobenzenesulfenamide (Nps), 2,4— dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2—nitro—4— methoxybenzenesulfenamide, triphenylmethylsulfenamide, and 3—nitropyridinesulfenamide (prs).

In certain embodiments, the substituent t on an oxygen atom is an oxygen protecting group (also ed to as a hydroxyl protecting group). Oxygen protecting groups include, but are not d to, —Raa, )2, —C(=O)SRaa, —C(=0)Raa, —C02Raa, — C(=O)N(Rbb)2, —C(=NRbb)Raa, —C(=NRbb)ORaa, —C(=NRbb)N(Rbb)2, —S(=0)Raa, —sozRaa, — Si<Raa>i —P<R°°>2, —P<R°°>3, —P<=0>2Raa, —P<=0><Raa>2, <0R°C>2, —P<=0>2N<Rbb>2, and — P(=O)(NRbb)2, wherein R”, Rbb, and RCC are as defined herein. Oxygen protecting groups are well known in the art and include those bed in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by nce.

Exemplary oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t—butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p— methoxybenzyloxymethyl (PMBM), (4—methoxyphenoxy)methyl (p—AOM), guaiacolmethyl (GUM), t—butoxymethyl, 4—pentenyloxymethyl (POM), siloxymethyl, 2— methoxyethoxymethyl (MEM), 2,2,2—trichloroethoxymethyl, bis(2—chloroethoxy)methyl, 2— (trimethylsilyl)ethoxymethyl ), tetrahydropyranyl (THP), 3— bromotetrahydropyranyl, tetrahydrothiopyranyl, l—methoxycyclohexyl, 4— methoxytetrahydropyranyl (MTHP), 4—methoxytetrahydrothiopyranyl, 4— methoxytetrahydrothiopyranyl S,S—dioxide, l—[(2—chloro—4—methyl)phenyl]—4— ypiperidin—4—yl (CTMP), l,4—dioxan—2—yl, tetrahydrofuranyl, tetrahydrothiofuranyl, ,4,5,6,7,7a—octahydro—7,8,8—trimethyl—4,7—methanobenzofuran—2—yl, l—ethoxyethyl, hloroethoxy)ethyl, l—methyl—l—methoxyethyl, l—methyl—l—benzyloxyethyl, l— methyl—l—benzyloxy—2—fluoroethyl, 2,2,2—trichloroethyl, 2—trimethylsilylethyl, 2— (phenylselenyl)ethyl, t—butyl, allyl, p—chlorophenyl, p—methoxyphenyl, 2,4—dinitrophenyl, benzyl (Bn), p—methoxybenzyl, 3,4—dimethoxybenzyl, 0—nitrobenzyl, p—nitrobenzyl, p— halobenzyl, 2,6—dichlorobenzyl, p—cyanobenzyl, ylbenzyl, 2—picolyl, 4—picolyl, 3— methyl—2—picolyl N—oxido, diphenylmethyl, p,p ’—dinitrobenzhydryl, 5—dibenzosuberyl, triphenylmethyl, (x—naphthyldiphenylmethyl, p—methoxyphenyldiphenylmethyl, di(p— methoxyphenyl)phenylmethyl, tri(p—methoxyphenyl)methyl, 4—(4’— bromophenacyloxyphenyl)diphenylmethyl, 4,4’,4"—tris(4,5— rophthalimidophenyl)methyl, 4,4’,4"—tris(levulinoyloxyphenyl)methyl, 4,4’,4"— tris(benzoyloxyphenyl)methyl, dazol—l—yl)bis(4’,4"—dimethoxyphenyl)methyl, l, l— bis(4—methoxyphenyl)—l’—pyrenylmethyl, 9—anthryl, 9—(9—phenyl)xanthenyl, 9—(9—phenyl— lO—oxo)anthryl, l,3—benzodisulfuran—2—yl, benzisothiazolyl oxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl ), dimethylthexylsilyl, t—butyldimethylsilyl (TBDMS), t— butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri—p—xylylsilyl, triphenylsilyl, ylmethylsilyl (DPMS), t—butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, WO 63468 methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p—chlorophenoxyacetate, 3— phenylpropionate, 4—oxopentanoate (levulinate), 4,4—(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, oxycrotonate, te, p— phenylbenzoate, 2,4,6—trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9— fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2—trichloroethyl carbonate (Troc), 2—(trimethylsilyl)ethyl carbonate (TMSEC), 2—(phenylsulfonyl) ethyl carbonate (Psec), 2—(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl Vinyl ate alkyl allyl carbonate, alkyl p—nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p—methoxybenzyl carbonate, alkyl 3,4—dimethoxybenzyl carbonate, alkyl 0—nitrobenzyl carbonate, alkyl p—nitrobenzyl carbonate, alkyl S—benzyl thiocarbonate, 4—ethoxy—l— napththyl carbonate, methyl carbonate, 2—iodobenzoate, 4—azidobutyrate, 4—nitro—4— methylpentanoate, 0—(dibromomethyl)benzoate, 2—formylbenzenesulfonate, 2— (methylthiomethoxy)ethyl, 4—(methylthiomethoxy)butyrate, 2— (methylthiomethoxymethyl)benzoate, 2,6—dichloro—4—methylphenoxyacetate, chloro— 4—( l , 1,3 ,3—tetramethylbutyl)phenoxyacetate, 2,4—bis( l , l—dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)—2—methyl—2—butenoate, 0— (methoxyacyl)benzoate, a—naphthoate, nitrate, alkyl N,N,N’,N’— tetramethylphosphorodiamidate, alkyl ylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4—dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).

In certain embodiments, the substituent present on an sulfur atom is an sulfur ting group (also referred to as a thiol protecting group). Sulfur protecting groups include, but are not limited to, —Raa, )2, —C(=O)SRaa, —C(=0)Raa, —C02Raa, — C(=O)N(Rbb)2, bb)Raa, —C(=NRbb)ORaa, —C(=NRbb)N(Rbb)2, —S(=0)Raa, —sozRaa, — Si(Raa)3, —P(R°°)2, —P(R°°)3, —P(=O)2Raa, —P(=0)(Raa)2, —P(=0)(OR°°)2, —P(=0)2N(Rbb)2, and — P(=O)(NRbb)2, wherein R”, Rbb, and RCC are as defined herein. Sulfur protecting groups are well known in the art and include those described in detail in ting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd n, John Wiley & Sons, 1999, incorporated herein by reference.

As used herein, a “leaVing group” is an art—understood term referring to a molecular fragment that departs with a pair of electrons in heterolytic bond cleavage, wherein the molecular fragment is an anion or l molecule. See, for example, Smith, March Advanced c try 6th ed. (501—502). Exemplary leaVing groups include, but are not d to, halo (e.g., chloro, bromo, iodo) and sulfonyl substituted hydroxyl groups (e.g., tosyl, mesyl, besyl).

These and other exemplary substituents are bed in more detail in the ed Description, Examples, Figures, and Claims. The invention is not ed to be limited in any manner by the above exemplary listing of substituents.

Other definitions As used herein, use of the phrase “at least one instance” refers to one instance, but also encompasses more than one instance, 6.57., for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 instances, and up to 100 instances.

An “amino acid” refers to natural and unnatural D/L alpha—amino acids, as well as natural and unnatural beta— and gamma— amino acids. A “peptide” refers to two amino acids joined by a peptide bond. A “polypeptide” refers to three or more amino acids joined by e bonds. An “amino acid side chain” refers to the group(s) pended to the alpha carbon (if an alpha amino acid), alpha and beta carbon (if a beta amino acid), or the alpha, beta, and gamma carbon (if a gamma amino acid). Exemplary amino acid side chains are ed herein; see, e.g., Table l of the Examples.

As used herein, a “polymer” refers to a compound comprised of at least 3 (e.g., at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, etc.) repeating covalently bound structural units.

“Conjugated” and “attached” refer to the covalent attachment of a group, and are used interchangeably herein.

As used herein, hilic” refers to the ability of a group to dissolve in fats, oils, lipids, and lipophilic non—polar solvents such as hexane or toluene. In l, a lipophilic group refers to an unsubstituted n—alkyl or unsubstituted n—alkenyl group having 6 to 50 carbon atoms, e.g., 6 to 40, 6 to 30, 6 to 20, 8 to 20, 8 to 19, 8 to 18, 8 to 17, 8 to 16, or 8 to 15 carbon atoms.

Use of the terms “structural isomer,77 4‘organic molecule,” and “inorganic molecule” are meant to encompass the common meaning of each term as known in the art.

As used , a “small organic molecule” or “small molecule” refers to an organic molecule with a molecular weight of 800 g/mol or less (e.g., less than 700 g/mol, less than 600 g/mol, less than 500 g/mol, less than 400 g/mol, less than 300 g/mol, less than 200 g/mol, less than 100 g/mol, between 50 to 800 g/mol, inclusive, between 100 to 800 g/mol, inclusive, or between 100 to 500 g/mol, inclusive). In certain embodiments, the small organic molecule is a therapeutically active agent such as a drug (e.g., a small organic le approved by the US. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)). The small organic molecule may also be complexed with a metal. In this instance, the small organic molecule is also referred to as an “small metallic molecule.” As used herein, a “large organic molecule” or “large molecule” refers to an organic compound with a molecular weight of greater than 800 g/mol (e.g., greater than 800 g/mol, greater than 900 g/mol, greater than 1000 g/mol, greater than 2000 g/mol, between 801 to 2000 g/mol, inclusive, between 900 to 2000 g/mol, inclusive, between 1000 to 2000 g/mol, inclusive, or n 801 to 1000 g/mol, inclusive). In certain embodiments, the large c molecule is a therapeutically active agent such as a drug (e.g., a large c le approved by the US. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)).The large organic molecule may also be complexed with a metal.

In this instance, the large organic molecule is also referred to as an “large organometallic compound.” As used herein, a “small inorganic molecule” refers to an nic compound with a molecular weight of 800 g/mol or less (e.g. less than 700 g/mol, less than 600 g/mol, less than 500 g/mol, less than 400 g/mol, less than 300 g/mol, less than 200 g/mol, less than 100 g/mol, between 50 to 800 g/mol, inclusive, between 100 to 800 g/mol, inclusive, or between 100 to 500 g/mol, inclusive). In certain embodiments, the small inorganic molecule is a therapeutically active agent such as a drug (e.g., a small inorganic le approved by the US. Food and Drug Administration as provided in the Code of l Regulations (CFR)).

As used herein, a “large inorganic molecule” refers to an inorganic compound with a molecular weight of greater than 800 g/mol (e.g., greater than 800 g/mol, greater than 900 g/mol, greater than 1000 g/mol, greater than 2000 g/mol, between 801 to 2000 g/mol, inclusive, between 900 to 2000 g/mol, inclusive, between 1000 to 2000 g/mol, inclusive, or between 801 to 1000 g/mol, ive). In certain embodiments, the large nic molecule is a therapeutically active agent such as a drug (e.g., a large inorganic molecule approved by the US. Food and Drug Administration as ed in the Code of Federal Regulations (CFR)).

As used herein, the term “salt” or “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue ty, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.

Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge et al., describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences (1977) 66: 1—19. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid on salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include e, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2—hydroxy—ethanesulfonate, ionate, lactate, laurate, lauryl e, malate, maleate, malonate, esulfonate, 2— naphthalenesulfonate, nicotinate, e, oleate, oxalate, palmitate, pamoate, pectinate, fate, ylpropionate, phosphate, picrate, te, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p—toluenesulfonate, undecanoate, valerate salts, and the like.

Salts d from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(C14alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, m, magnesium, and the like. r pharmaceutically acceptable salts e, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, sulfonate and aryl sulfonate. r pharmaceutically acceptable salts include salts formed from the mization of an amine using an appropriate electrophile, e. 57., an alkyl halide, to form a quarternized alkylated amino salt.

Brief ption of the Drawings Figure 1 depicts the structural design and optimization through in viva evaluation in mice. Single amino acid—based lipid derivatives were tested at a dose of lmg/kg in mice, which indicated that lysine was a favorable amino acid. Lysine—based peptide and polypeptide—lipid derivatives were then investigated at the same dose. The hit rate was improved from 1.7% to 23% (including those compounds not screened due to particle instability or no entrapment of siRNA). The top hits and their analogs were explored at a lower dose of 0.1 mg/kg, which led to selection of cKK—E12 as the lead compound. K—ElZ; K: abbreviation of lysine, E: e, A: aldehyde, 0: acrylate, 12: carbon tail length. cKK— E12; c: cyclic; Control, phosphate—buffered saline.

Figure 2 depicts the bio—distribution of free Cy5.5—labled siRNA and Cy5.5— labled siRNA—cKK—E12 formulation in mice at 1 hr and 24 hr.

Figure 3 depicts the silencing s of apolipoproteins on cKK—E12 in HeLa cells. Apolipoproteins including ApoA—I (recombinant Human ApoA—I n), ApoA—II (native Human ApoA—II protein), ApoB (native Human ApoB protein), ApoC—I (native Human ApoC—I protein), ApoC—II (native Human ApoC—II protein), ApoC—III (native Human II protein), ApoE (native Human ApoE protein), ApoE2 (recombinant Human ApoE2 protein), ApoE3 (recombinant Human ApoE3 protein), ApoE4 (recombinant Human ApoE4 protein), ApoH (native Human ApoH protein).

Figure 4 depicts the effects of ApoE on gene silencing and cell uptake. A).

Silencing effects of ApoE on cKK—ElZ, cKK—AlZ, and 2 in vitro (siRNA: 50 ng/well). With addition of ApoE, the order of silencing effects was cKK—E12 > cKK—A12 > Z, correlating well with in vivo activity. B). Cellular internalization of 2 with Alex—647 labeled siRNA after 3 hr of incubation is demonstrated by HT automated confocal microscopy. ApoE enhanced cell uptake and endosomal escape of 2; Scale bar: 20 Detailed Description of Certain Embodiments of the Invention Described herein are inventive compounds and compositions, certain embodiments of which involve conjugation of various groups, such as ilic groups, to an amino or amide group of an amino acid, a linear or cyclic e, a linear or cyclic polypeptide, or structural isomer thereof, to e compounds of the present invention, collectively ed to herein as “APPLs”. Such APPLs are deemed useful for a variety of applications, such as, for example, improved nucleotide delivery.

Exemplary APPLs include, but are not limited to, compounds of Formula (I), (II), (III), (IV), (V), and (VI), and salts thereof, as described herein: (11) R1 B2 R1 Q R2 Q (1V) 2 Q R2 Q R\ \ N 1 1 R2'—N/ R1 R —< R R2 Q R1 (V) (VI) wherein m, n, p, R1, R2, R3, R4, R5, R8, Z, W, Y, and Z are as defined herein.

Various RL groups, e.g., lipophilic groups, may be attached to the APPL Via conjugation of a primary or secondary amino group or amide of the amino acid, peptide, or polypeptide precursor, or structural isomer f, with an epoxide, thiirane, or ine of formula (i—X), Michael addition to an OL,B—unsaturated ester, thioester, or amide of formula (ii— X), or reductive amination to an aldehyde of formula ) (Scheme 1).

Scheme 1.

H i RL (iii-x) L R'- g—ill—g or g—NHZ i> §_Nr_§ §_H_/R g—N_/ mono addition bis addition Thus, in the broadest , the present invention provides APPLs, and in n embodiments, nds of Formula (I), (II), (III), (IV), (V), and (VI), comprising at least one instance of a group ed thereto of the formula: H\ R'- RI $4 (1) (ii) (iii) wherein: each instance of R’ is independently en or optionally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, ally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, n RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted C150 heteroalkyl, optionally substituted C250 alkenyl, optionally substituted C250 heteroalkynyl, or a polymer.

Various embodiments of formula (i), (ii), and (iii), and les RL, RP, X, and Y are described in greater detail herein.

Compounds ofFormula (I) Compounds of Formula (I) encompasses amino acids, linear peptides, and linear polypeptides which comprise one or more sites of conjugation, e.g., to the terminal amino group, to an amino substituent, and/or to an imino en, of a group of formula (i), (ii), or (iii). imino nitrogens Thus, in one aspect, provided is a compound of Formula (I): ” (I) or salt thereof; wherein: n is 0 or is an integer between 1 and 100,000, inclusive; each instance of m is independently l, 2, or 3; each instance of Z is independently O, S, or NRZ, wherein RZ is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii); each instance of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally tuted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, n, —ORA1, )2, or —SRA1; wherein each occurrence of RAl is ndently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally tuted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to an sulfur atom, a nitrogen protecting group when attached to a nitrogen atom, or two RAl groups are joined to form an optionally substituted heterocyclic or optionally substituted heteroaryl ring; R2 is a group of formula (i), (ii), or (iii); R3 is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally substituted aryl, a nitrogen protecting group, or a group of the a (i), (ii), or (iii); or R3 and an R1 group are joined to form an optionally substituted 5—6 membered heterocyclic ring; R4 is —ORA4, —N(RA4)2, or —SRA4; wherein each occurrence of RA4 is independently hydrogen, ally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen ting group when attached to an oxygen atom, a sulfur protecting group when attached to an sulfur atom, a nitrogen protecting group when attached to a nitrogen atom, or two RA4 groups are joined to form an optionally substituted heterocyclic or optionally substituted heteroaryl ring; R5 is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted aryl, or a nitrogen protecting group; Formulae (i), (ii), and (iii) are: RQ—YRP é—flR. gJRL (i) (ii) (iii) wherein: each instance of R’ is independently hydrogen or optionally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; 2012/062222 Y is O, S, NRY, n RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when ed to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, optionally substituted C250 alkynyl, ally substituted heteroC1_50 alkyl, optionally substituted C2_50 alkenyl, optionally substituted C2_50 alkynyl, or a polymer.

In certain embodiments, when n is greater than 10, then neither R2 nor R3 is a group of the formula (iii). In certain ments, when n is greater than 9, then neither R2 nor R3 is a group of the formula (iii). In certain embodiments, when n is greater than 8, then neither R2 nor R3 is a group of the a (iii). In certain embodiments, when n is greater than 7, then neither R2 nor R3 is a group of the formula (iii). In certain embodiments, when n is greater than 6, then neither R2 nor R3 is a group of the formula (iii). In n embodiments, when n is greater than 5, then neither R2 nor R3 is a group of the formula (iii).

In certain ments, when n is greater than 4, then neither R2 nor R3 is a group of the formula (iii). In certain embodiments, when n is greater than 3, then neither R2 nor R3 is a group of the formula (iii). In certain embodiments, when n is greater than 2, then neither R2 nor R3 is a group of the formula (iii). In n embodiments, when n is greater than 1, then neither R2 nor R3 is a group of the formula (iii). In certain embodiments, neither R2 nor R3 is a group of the a (iii).

In certain embodiments, wherein n is 0 and Z is 0, one or more of the ing compounds are excluded: 3 0 R2’ OH 2 R2 R3\ VL R\N OH [ll NH2 HN/WJkOH \N/YkOH R2 K/NH K/N\RZ K/N and \R2 , , , , and salts thereof; wherein R2 is a group of the formula (i), R3 and R6 are independently hydrogen or a group of formula (i), and Y is O.

As generally defined above, n is 0 or is an integer between 1 and 0, inclusive. It is thus understood that Formula (I) encompasses amino acids conjugated to a lipid group, as well as linear peptides and linear polypeptides conjugated to lipid groups.

In n embodiments, n is 0 or is an integer n 1 and , inclusive.

In certain embodiments, n is 0 or is an integer between 1 and 80,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 70,000, inclusive. In n embodiments, n is 0 or is an integer between 1 and 50,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 40,000, inclusive. In certain embodiments, n is 0 or is an r between 1 and , ive. In certain embodiments, n is 0 or is an r between 1 and 20,000, inclusive. In certain ments, n is 0 or is an integer between 1 and 10,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 9,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 8,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 7,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 6,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 5,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 4,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 3,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 2,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 1,000, inclusive. In certain embodiments, n is 0 or is an integer n 1 and 900, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 800, inclusive. In certain embodiments, n is 0 or is an r between 1 and 700, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 600, ive. In certain embodiments, n is 0 or is an integer between 1 and 500, inclusive. In certain embodiments, n is 0 or is an r between 100 and 80,000, inclusive. In certain embodiments, n is 0 or is an integer between 200 and , ive.

In certain ments, n is 0 or is an integer between 300 and 80,000, inclusive. In certain embodiments, n is 0 or is an integer between 400 and 80,000, inclusive. In certain embodiments, n is 0 or is an integer between 500 and 80,000, inclusive. In certain embodiments, n is 0 or is an integer between 500 and 40,000, inclusive. In certain embodiments, n is 0 or is an integer between 500 and 30,000, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 400, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 300, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 200, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 100, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 75, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 50, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 25, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 15, inclusive. In certain embodiments, n is 0 or is an r n 1 and 10, I nclusive. In certain embodiments, n is 0, l, 2, 3, 4, , 6, 7, 8, 9, or 10.

For example, when n is 0, the compound of Formula (I) is a compound of the Formula (I—a): Fr Z R2—N R4 R1 <I-a> or salt f.

In n embodiments, when n is l, the nd of Formula (I) is a compound of the Formula (I—b): Fr Z t5 Z RZ—N N R4 m m R1 R1 (Lb) or salt thereof.

In certain embodiments, when n is 2, the compound of a (I) is a compound of the Formula (I—c): FI<3 z F|<5 2 1'25 z RZ—N N N R4 m m m or salt thereof.

In certain embodiments, when n is 3, the compound of Formula (I) is a compound of the Formula (I—d): R3 z R5 z R5 z R5 z Fez—I l l l R4 m m m m R1 R1 R1 R1 (1-d) or salt thereof.

In certain embodiments, when n is 4, the nd of Formula (I) is a compound of the a (I—e): F|<3z|52F|<5ZIT5z|5z RZ—N.( )JJ—NE j,U—Né l’U—NE )J—NWJLR“m m m m m R R1 R1 R1 R1 (1-6) or salt thereof.

As generally defined above, each instance of m is independently l, 2, or 3. In certain embodiments, at least one instance of m is 1. In n embodiments, each instance of m is 1. In n embodiments, at least one instance of m is 2. In certain embodiments, at least one instance of m is 3.

As generally defined above, each instance of R’ is independently hydrogen or optionally tuted alkyl. In certain ments, at least one instance of R’ is hydrogen.

In certain embodiments, at least two instances of R’ is hydrogen. In certain embodiments, each instance of R’ is hydrogen. In certain embodiments, at least one instance of R’ is optionally substituted alkyl, e.g., methyl. In certain embodiments, at least two ces of R’ is optionally substituted alkyl, e.g., methyl. In certain embodiments, one ce of R’ is optionally substituted alkyl, and the rest are hydrogen.

As generally defined above, each instance of Z is independently O, S, or NRZ, wherein RZ is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii). In certain embodiments, at least one instance of Z is O. In certain embodiments, each instance of Z is O. In certain embodiments, at least one instance of Z is S. In n embodiments, each instance of Z is S.

In certain embodiments, at least one ce of Z is NRZ. In certain embodiments, each instance of Z is NRZ. In n embodiments, each instance of RZ is independently hydrogen or a group of the formula (i), (ii), or (iii). 2012/062222 As generally defined above, each instance of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, ally substituted alkynyl, optionally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, ally substituted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1.

In certain embodiments, at least one instance of R1 is optionally substituted alkyl, optionally substituted alkenyl, ally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

In certain embodiments, at least one instance of R1 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally substituted C2_6alkyl, optionally substituted C3_6alkyl, optionally substituted C4_6alkyl, optionally substituted C4_5alkyl, or ally tuted C34alkyl.

In certain embodiments, at least one instance of R1 is optionally substituted alkenyl, e.g., optionally substituted C2_6alkenyl, optionally tuted C3_6alkenyl, optionally tuted C4_6alkenyl, ally substituted C4_5alkenyl, or ally substituted C3- 4alkenyl.

In certain embodiments, at least one instance of R1 is optionally substituted alkynyl, e.g., optionally tuted C2_6alkynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally tuted C3- 4alkynyl.

In certain embodiments, at least one instance of R1 is optionally substituted carbocyclyl, e.g., optionally substituted C3_10 carbocyclyl, optionally substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally substituted C6 carbocyclyl.

In certain embodiments, at least one instance of R1 is optionally substituted heterocyclyl, e.g., optionally substituted 3—14 membered cyclyl, optionally substituted 3—10 membered heterocyclyl, ally substituted 5—8 membered cyclyl, optionally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In certain embodiments, at least one instance of R1 is optionally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, at least one instance of R1 is ally substituted heteroaryl, e.g., ally substituted 5—14 membered heteroaryl, optionally substituted 5—10 2012/062222 membered heteroaryl, optionally tuted 5—6 membered heteroaryl, optionally substituted membered heteroaryl, or optionally substituted 6 membered heteroaryl.

In any of the above embodiments, the R1 alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or aryl group may be substituted, for example, with an optionally tuted amino group (e.g., —NR6R7), an optionally substituted hydroxyl group (e.g., —OR6), an optionally substituted thiol group (e.g., —SR6), or with a group of formula (i), (ii), or (iii), n each instance of R6 and R7 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen ting group when attached to a nitrogen atom, an oxygen ting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or a group of a (i), (ii), or (iii).

For example, in certain embodiments, at least one ce of R1 is an alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl group substituted with an amino group of the formula —N(R6)(R7). In that instance, in certain embodiments, at least one instance of R1 is a group of formula: wherein: L is an optionally substituted alkylene, optionally substituted alkenylene, ally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, ally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, or optionally substituted heteroarylene, or combination thereof, and R6 and R7 are independently selected from the group ting of hydrogen, optionally substituted alkyl, optionally tuted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, and a nitrogen protecting group; provided at least one instance of R6 and R7 is a group of the formula (i), (ii), or (iii): 2012/062222 . R‘ XRL RQ—YRP g—<R- § 0 R'- R' or §_/ (1) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In certain embodiments, at least two instances of R1 is a group of a (iv).

In certain embodiments, at least three instances of R1 is a group of formula (iv). In certain embodiments, at least four instances of R1 is a group of formula (iv). In certain embodiments, at least five instances of R1 is a group of formula (iv). In certain embodiments, each instance of R1 is a group of formula (iv).

In certain ments, L is an optionally tuted alkylene; e.g., optionally tuted C1_50alkylene, optionally tuted C1_40alkylene, optionally substituted C1- lene, optionally substituted C1_20alkylene, optionally substituted C4_20alkylene, optionally tuted C6_20alkylene, optionally substituted Cg_20all<ylene, optionally substituted alkylene, optionally substituted C1_6alkylene, optionally substituted C2- 6alkylene, optionally substituted C3_6alkylene, optionally substituted C4_6alkylene, optionally substituted C4_5alkylene, or optionally substituted C3_4alkylene.

In certain embodiments, L is an optionally substituted alkenylene, e.g., optionally substituted lkenylene, optionally substituted lkenylene, optionally substituted lkenylene, optionally substituted enylene, optionally tuted C4- goalkenylene, optionally substituted C6_20alkenylene, optionally substituted Cg_20all<enylene, optionally substituted C10_20alkenylene, optionally substituted C2_6alkenylene, optionally substituted C3_6alkenylene, optionally substituted C4_6alkenylene, optionally substituted C4- ylene, or optionally substituted C3_4alkenylene.

In certain embodiments, L is an optionally substituted alkynylene, e.g., optionally substituted C2_50alkynylene, optionally substituted C2_40alkynylene, optionally substituted C2_30alkynylene, optionally substituted Cnoalkynylene, optionally substituted C4- goalkynylene, optionally substituted C6_20alkynylene, optionally substituted Cg_20all<ynylene, ally substituted C10_20alkynylene, optionally substituted C2_6alkynylene, optionally substituted C3_6alkynylene, optionally substituted C4_6alkynylene, optionally substituted C4- 5alkynylene, or ally substituted C3_4alkynylene.

In certain embodiments, L is an optionally substituted heteroalkylene; e.g., optionally substituted heteroC1_50alkylene, optionally substituted heteroC1_40alkylene, 2012/062222 optionally substituted heteroC1_30alkylene, optionally tuted heteroC1_20alkylene, optionally substituted heteroC4_20alkylene, optionally substituted heteroC6_20alkylene, optionally substituted heterng_20all<ylene, optionally substituted heteroC10_20alkylene, optionally substituted heteroC1_6alkylene, optionally substituted heteroC2_6alkylene, optionally substituted heteroC3_6alkylene, optionally tuted heteroC4_6alkylene, optionally substituted heteroC4_5alkylene, or optionally tuted heteroC3_4alkylene.

In certain embodiments, L is an optionally substituted alkenylene, e.g., optionally tuted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, optionally substituted heteroC2_30alkenylene, optionally substituted heteroC2_20alkenylene, optionally substituted C4_20alkenylene, optionally substituted heteroC6_20alkenylene, optionally substituted heterng_20all<enylene, optionally substituted heteroC10_20alkenylene, optionally tuted heteroC2_6alkenylene, optionally substituted heteroC3_6alkenylene, optionally substituted heteroC4_6alkenylene, ally substituted heteroC4_5alkenylene, or optionally substituted heteroC3_4alkenylene.

] In certain ments, L is an optionally substituted alkynylene, e.g., optionally substituted heteroC2_50alkynylene, optionally substituted heteroC2_40alkynylene, optionally substituted heteroC2_30alkynylene, optionally substituted heteroC2_20alkynylene, optionally substituted heteroC4_20alkynylene, optionally substituted heteroC6_20alkynylene, optionally tuted heterng_20alkynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, optionally substituted C3_6alkynylene, optionally substituted heteroC4_6alkynylene, optionally tuted heteroC4_5alkynylene, or optionally substituted heteroC3_4alkynylene.

In n embodiments, L is an optionally substituted carbocyclylene, e.g., optionally substituted C340 carbocyclylene, ally substituted C5_g carbocyclylene, optionally substituted C5_6 carbocyclylene, optionally substituted C5 carbocyclylene, or optionally substituted C6 carbocyclylene.

In certain embodiments, L is an optionally substituted heterocyclylene, e.g., optionally substituted 3— l4 membered heterocyclylene, optionally substituted 3—10 membered heterocyclylene, optionally substituted 5—8 membered heterocyclylene, optionally substituted —6 membered heterocyclylene, optionally substituted 5 ed heterocyclylene, or optionally substituted 6 membered cyclylene.

In certain embodiments, L is an optionally substituted arylene, e.g., optionally substituted phenylene.

In certain embodiments, L is an optionally substituted heteroarylene, e.g., optionally substituted 5— l4 membered arylene, optionally substituted 5—10 membered heteroarylene, optionally substituted 5—6 membered heteroarylene, optionally substituted 5 membered heteroarylene, or ally substituted 6 membered heteroarylene.

For example, in certain embodiments, wherein L is an optionally tuted ne group, the group of formula (iv) is a group of the formula: wherein q is an integer between 1 and 50, inclusive.

In certain embodiments, q is an integer between 1 and 40, inclusive. In certain embodiments, q is an integer between 1 and 30, inclusive. In certain embodiments, q is an integer between 1 and 20, inclusive. In certain embodiments, q is an integer between 4 and , inclusive. In certain embodiments, q is an integer between 6 and 20, inclusive. In certain ments, q is an integer n 8 and 20, inclusive. In certain embodiments, q is 1. In certain embodiments, q is 2. In certain embodiments, q is 3. In certain embodiments, q is 4. In certain ments, q is 5. In certain embodiments, q is 6. In certain embodiments, q is 7. In certain embodiments, q is 8. In certain embodiments, q is 9. In certain embodiments, q is 10.

In certain embodiments, both R6 and R7 are hydrogen. In certain embodiments, R6 is hydrogen and R7 is a group of the formula (i), (ii), or (iii). In n embodiments, R6 is hydrogen and R7 is a group of the formula (i). In certain ments, R6 is hydrogen and R7 is a group of the formula (ii). In n embodiments, R6 is hydrogen and R7 is a group of the formula (iii). In n embodiments, both R6 and R7 are independently a group of the formula (i), (ii), or (iii). In certain embodiments, both R6 and R7 are independently a group of the formula (i). In certain embodiments, both R6 and R7 are independently a group of the formula (ii). In n embodiments, both R6 and R7 are independently a group of the a (iii). In certain ments, both R6 and R7 are the same group, selected from a group of the formula (i), (ii), or (iii).

It is understood that R1 encompasses amino acid side chains such as exemplified in Table l of the Examples. In certain embodiments, R1 is a group selected from any one of the amino acid side chain groups listed therein.

In certain embodiments, each instance of R1 is the same. In certain embodiments, at least one R1 group is different. In certain embodiments, each R1 group is different. 2012/062222 As generally d above, R2 is a group of the formula (i), (ii), or (iii): R‘ XRL RQ—YRP é—flR. § 0 RL R. or ;_/ (i) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In certain embodiments, R2 is a group of the formula (i). In certain embodiments, R2 is a group of the formula (ii). In certain ments, R2 is a group of the formula (iii).

As generally defined above, R3 is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, a nitrogen ting group, or a group of the formula (i), (ii), or (iii); optionally wherein R3 and an R1 group are joined to form an optionally tuted 5—6 membered heterocyclic ring; In certain embodiments, R3 is hydrogen. In certain embodiments, R3 is optionally substituted alkyl; e.g., ally tuted C1_6alkyl, optionally substituted C2- 6alkyl, optionally substituted C3_6alkyl, optionally substituted C4_6alkyl, optionally substituted C4_5alkyl, or optionally substituted C34alkyl.

In certain embodiments, R3 is optionally substituted alkenyl, e.g., optionally substituted C2_6alkenyl, ally substituted C3_6alkenyl, optionally substituted C4_6alkenyl, optionally substituted kenyl, or optionally substituted C3_4alkenyl.

In certain embodiments, R3 is ally substituted alkynyl, e.g., optionally substituted kynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally tuted C3_4alkynyl.

In certain embodiments, R3 is optionally substituted carbocyclyl, e.g., optionally substituted C340 carbocyclyl, optionally substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally substituted C6 yclyl.

In certain embodiments, R3 is optionally substituted heterocyclyl, e.g., optionally substituted 3— l4 membered heterocyclyl, ally substituted 3— 10 membered heterocyclyl, optionally substituted 5—8 membered heterocyclyl, optionally substituted 5—6 membered heterocyclyl, optionally tuted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In n embodiments, R3 is optionally tuted aryl, e.g., ally substituted phenyl.

In certain embodiments, R3 is optionally substituted heteroaryl, e.g., optionally substituted 5— l4 ed heteroaryl, optionally substituted 5—10 membered heteroaryl, optionally substituted 5—6 membered heteroaryl, optionally substituted 5 ed heteroaryl, or optionally substituted 6 membered heteroaryl.

In certain embodiments, R3 is a nitrogen protecting group.

In certain ments, R3 is group of the formula (i), (ii), or (iii). In certain embodiments, R3 is group of the formula (i). In certain embodiments, R3 is group of the formula (ii). In certain embodiments, R3 is group of the formula (iii).

In certain ments, R3 and an adjacent R1 group are joined to form an optionally substituted 5—6 membered heterocyclic ring, e.g., a 5—membered heterocyclic ring, e.g., an optionally substituted pyrrolidinyl ring.

In n embodiments, R3 is hydrogen and R2 is a group of the formula (i), (ii), or (iii). In certain embodiments, R3 is hydrogen and R2 is a group of the formula (i). In certain embodiments, R3 is hydrogen and R2 is a group of the formula (ii). In certain embodiments, R3 is hydrogen and R2 is a group of the formula (iii). In n embodiments, both R2 and R3 are independently a group of the formula (i), (ii), or (iii). In certain embodiments, both R2 and R3 are ndently a group of the formula (i). In certain embodiments, both R2 and R3 are independently a group of the formula (ii). In certain ments, both R2 and R3 are independently a group of the formula (iii). In certain embodiments, both R2 and R3 are the same group, selected from a group of the formula (i), (ii), or (iii).

As generally defined above, R4 is —ORA4, —N(RA4)2, or —SRA4; wherein each occurrence of RA4 is independently hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to an sulfur atom, a en protecting group when attached to a nitrogen atom, or two RA4 groups are joined to form an optionally substituted heterocyclic or optionally substituted heteroaryl ring.

In certain embodiments, R4 is —ORA4, wherein RA4 is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, ally tuted l, optionally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or an oxygen protecting group. In certain embodiments, RA4 is hydrogen or optionally substituted alkyl. In certain embodiments, RA4 is hydrogen.

In certain embodiments, R4 is —N(RA4)2, wherein each occurrence of RA4 is ndently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, or two RA4 groups are joined to form an optionally substituted heterocyclic or ally substituted heteroaryl ring. In certain ments, at least one instance of RA4 is hydrogen or optionally substituted alkyl. In certain embodiments, at least one instance of RA4 is hydrogen.

In certain embodiments, R4 is —SRA4, wherein RA4 is hydrogen, optionally substituted alkyl, ally tuted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or sulfur protecting group. In certain embodiments, RA4 is hydrogen or optionally tuted alkyl. In certain embodiments, RA4 is hydrogen.

] As lly d above, R5 is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group. In certain embodiments, at least one instance of R5 is hydrogen. In certain embodiments, each instance of R5 is hydrogen.

Various combinations of the above embodiments of a (I) are contemplated herein.

For example, in certain embodiments, wherein each instance of m is l and each instance of Z is O, the compound of Formula (I) is a compound of Formula (I—f): 3 I5 R4 “ (1-f) or salt f. In certain embodiments, at least one R1 is a group of formula (iV). In certain embodiments, R2 is a group of formula (i). In certain embodiments, R2 is a group of formula (ii). In certain embodiments, R2 is a group of formula (iii). In certain embodiments, R3 is a group of formula (i). In certain ments, R3 is a group of formula (ii). In certain ments, R3 is a group of a (iii). In certain embodiments, R4 is —ORA4. In certain embodiments, R5 is hydrogen. In certain embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

For example, in certain embodiments of a (I—f), wherein each instance of R1 is a group of the formula (iv), provided is a compound of Formula (I—fl): (I—fl) or salt thereof. In certain ments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain ments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii).

In certain embodiments of Formula (I—f), wherein R2 is a group of formula (i), the compound is of Formula (I—f2): RL I ‘ N RPY—/ R 1 ” (1-f2) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iv). In n embodiments, R3 is a group of formula (i). In certain embodiments, R3 is a group of formula (ii). In n embodiments, R3 is a group of formula (iii). In certain embodiments, R4 is — ORA4. In certain embodiments, R5 is hydrogen. In certain embodiments, n is 0. In n embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

] For example, in certain embodiments of Formula (I—f2), wherein each instance of R1 is a group of the a (iv), provided is a compound of Formula (I—f3): (I—f3) or salt thereof. In certain embodiments, L is an optionally tuted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii).

In certain embodiments of Formula (I—f), wherein R2 and R3 are each independently a group of formula (i), the compound is of Formula (I—f4): | R4 ” (I—f4) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In certain embodiments, R4 is —ORA4. In certain embodiments, R5 is hydrogen. In n embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

] For example, in certain embodiments of Formula (I—f4), wherein each instance of R1 is a group of the a (iV), ed is a compound of a (I—f5): RL 0 RPYfi/ o F|e5 R4 RL\ N RPY_/ L\ /R6 L R5 ‘N’ Ii] I n R7 R7 (I—f5) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii).

In certain ments of Formula (I—f), wherein R2 is a group of a (ii), the compound is of Formula (I—f6): RLX n (I—f6) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In n embodiments, R3 is a group of formula (i). In n embodiments, R3 is a group of formula (ii). In certain embodiments, R3 is a group of formula (iii). In certain embodiments, R4 is — ORA4. In certain embodiments, R5 is hydrogen. In certain embodiments, n is 0. In n embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In n embodiments, n is 4. In certain embodiments, n is 5.

] For example, in certain embodiments of Formula (I—f6), wherein each instance of R1 is a group of the formula (iV), provided is a compound of Formula (I—f7): (1-f7 ) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain ments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii).

In certain embodiments of Formula (I—f), wherein R2 and R3 are independently a group of formula (ii), the compound is of Formula (I—f8): RLX o o R5 l R4 0V—N RLX n (I—f8) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In certain embodiments, R4 is —ORA4. In certain embodiments, R5 is hydrogen. In certain embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

For example, in certain embodiments of a (I—f8), wherein each instance of R1 is a group of the formula (iV), ed is a compound of Formula (I—f9): (1-f9) or salt thereof. In n embodiments, L is an optionally substituted ne. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii).

In certain embodiments of Formula (I—f), wherein R2 is a group of formula (iii), the compound is of a (I—f10): ” (I—f10) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In certain embodiments, R3 is a group of formula (i). In certain embodiments, R3 is a group of a (ii). In certain embodiments, R3 is a group of formula (iii). In certain ments, R4 is — ORA4. In certain embodiments, R5 is hydrogen. In certain embodiments, n is 0. In n embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

For e, in certain embodiments of Formula (I—f10), wherein each instance of R1 is a group of the formula (iV), provided is a compound of Formula (I—fl l): (I—fl 1) or salt f. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of a (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii).

] In n embodiments of Formula (I—f), wherein R2 and R3 are independently a group of formula (iii), the nd is of Formula (I—f12): RL 0 R5 W l R4 RL R1 n (I—f12) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In certain embodiments, R4 is —ORA4. In certain embodiments, R5 is hydrogen. In certain embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

For example, in certain embodiments of Formula (I—f12), wherein each instance of R1 is a group of the formula (iV), provided is a compound of Formula (I—fl3): (I—fl 3) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In n embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of a (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). nds ofFormula (II) nds of Formula (11) may be prepared Via internal cyclization of the addition product of a primary or secondary amine or amide of an amino acid, peptide, or polypeptide, and an epoxide, thiirane, or aziridine of formula (i—X) (Scheme 2).

Scheme 2.

] Compounds of Formula (11) may encompass additional sites of conjugation, e.g., the secondary amino group, appended to a group attached to the secondary amino group, an amino substituent, and/or an imino nitrogen, to a group of formula (i), (ii), or (iii): w w :'\'/\'/': R1VLY [RE-":L 1 . \N : \HLY .- ----- R' : 5 '7: R' RWAY R' _\l_: RL '____B_iR8’N RL R8’N\H<RL R' R' R' secondary amino group amino substituents imino nitrogens Thus, in a second aspect, provided is a compound of Formula (II): or salt thereof; wherein: each instance of R’ is independently en or optionally substituted alkyl; each instance of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted aryl, halogen, —ORA1, —N(RA1)2, or —SRA1; wherein each occurrence of RAl is independently hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to an sulfur atom, a nitrogen protecting group when attached to a nitrogen atom, or two RAl groups are joined to form an ally substituted heterocyclic or optionally tuted heteroaryl ring; R8 is hydrogen, a group of the formula (i), (ii), or (iii), or a group of the formula (V): R3 $5 N g ” (V) wherein Z, R2, R3, R5, m, and n are as defined for Formula (I); or R8 and an R1 group are joined to form an optionally substituted 5—6 membered heterocyclic ring; each instance of W is independently O, S, or NRW, n RW is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii); and each instance of Y is independently O, S, or NRY, wherein RY is hydrogen, optionally tuted alkyl, ally substituted alkenyl, optionally tuted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Formulae (i), (ii), and (iii) are: R‘ XRL RQ—YRP §—§RI § 0 R'- R. or §_/ (1) (ii) (iii) wherein: X is O, S, NRX, wherein RX is hydrogen, ally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, ally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a en protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally substituted heteroC2_50 alkenyl, optionally substituted heteroC2_50 alkynyl, or a polymer.

In certain embodiments, wherein Y is O and W is O, the following compounds are ically excluded: 0 o o 0 0 o 0 R60 0 N\)\ ,N\)\ ,N Me/ RL, R8 RL, R8 RL, \RL, 0 o (R60)OZS o o R8,N\)\ R50 R8,N¢\ RL, RL, wherein R8 and R6 are independently hydrogen or a group of formula (i), and salts thereof.

In certain embodiments, at least one instance of RW, R2, R3, R6 or R8 is a , R7, group of the formula (i), (ii), or (iii).

As generally defined above, each instance of R’ is independently hydrogen or optionally substituted alkyl. In certain embodiments, at least one instance of R’ is hydrogen.

In certain embodiments, at least two instances of R’ is hydrogen. In certain embodiments, each instance of R’ is hydrogen. In certain embodiments, at least one instance of R’ is optionally substituted alkyl, e.g., methyl. In certain embodiments, at least two instances of R’ is optionally tuted alkyl, e.g., methyl. In certain embodiments, one instance of R’ is ally tuted alkyl, and the rest are en.

] As generally defined above, each instance of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, WO 63468 optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1.

In certain embodiments, at least one instance of R1 is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

] In certain embodiments, at least one instance of R1 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally substituted C2_6alkyl, optionally substituted C3_6alkyl, optionally substituted kyl, optionally substituted C4_5alkyl, or optionally substituted yl.

In n embodiments, at least one instance of R1 is optionally tuted alkenyl, e.g., optionally substituted C2_6alkenyl, optionally substituted C3_6alkenyl, ally tuted C4_6alkenyl, optionally substituted C4_5alkenyl, or optionally substituted C3- 4alkenyl.

In certain embodiments, at least one instance of R1 is optionally substituted l, e.g., optionally substituted C2_6alkynyl, optionally substituted kynyl, optionally tuted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally substituted C3- In certain embodiments, at least one instance of R1 is optionally tuted carbocyclyl, e.g., optionally substituted C3_10 carbocyclyl, optionally tuted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally substituted C6 carbocyclyl.

In certain embodiments, at least one ce of R1 is ally substituted heterocyclyl, e.g., optionally substituted 3—14 membered heterocyclyl, optionally substituted 3—10 membered heterocyclyl, optionally substituted 5—8 membered heterocyclyl, optionally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In certain embodiments, at least one instance of R1 is optionally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, at least one instance of R1 is optionally substituted heteroaryl, e.g., optionally substituted 5—14 membered heteroaryl, optionally substituted 5—10 membered aryl, optionally substituted 5—6 membered heteroaryl, optionally substituted membered heteroaryl, or optionally tuted 6 membered heteroaryl.

In any of the above embodiments, the R1 alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl group may be substituted, for example, with an optionally substituted amino group (e.g., —NR6R7), an optionally tuted hydroxyl group (e.g., —OR6), an optionally substituted thiol group (e.g., —SR6), or with a group of formula (i), (ii), or (iii), wherein each instance of R6 and R7 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a en protecting group when attached to a en atom, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or a group of formula (i), (ii), or (iii).

For example, in certain embodiments, at least one instance of R1 is an alkyl, alkenyl, alkynyl, yclyl, cyclyl, aryl, or heteroaryl group substituted with an amino group of the formula —N(R6)(R7). In that instance, in certain embodiments, at least one instance of R1 is a group of formula: é—L—Nf R7 (iv) wherein: L is an optionally substituted alkylene, optionally tuted alkenylene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, ally tuted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, or optionally tuted heteroarylene, or combination thereof, and R6 and R7 are independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, ally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally tuted heteroaryl, and a nitrogen protecting group; provided at least one instance of R6 and R7 is a group of the formula (i), (ii), or (iii): (i) (ii) (iii) n R’, X, Y, RL, and RP are as defined herein.

WO 63468 In certain embodiments, at least two instances of R1 is a group of formula (iv).

In certain embodiments, at least three instances of R1 is a group of a (iv). In certain embodiments, at least four instances of R1 is a group of formula (iv). In certain ments, at least five ces of R1 is a group of formula (iv). In certain embodiments, each instance of R1 is a group of formula (iv).

In certain embodiments, R1 alpha to the group —C(=W)—Y— is a group of formula (iv).

In certain embodiments, at least one instance of R1 provided in group R8 is a group of formula (iv). In certain embodiments, at least two instances of R1 provided in group R8 is a group of formula (iv). In certain embodiments, at least three instances of R1 provided in group R8 is a group of a (iv). In certain embodiments, at least four instances of R1 provided in group R8 is a group of formula (iv). In certain embodiments, at least five instances of R1 provided in group R8 is a group of a (iv). In certain embodiments, each instance of R1 provided in group R8 is a group of formula (iv).

In certain embodiments, L is an optionally substituted alkylene; e.g., optionally substituted C1_50alkylene, optionally substituted C1_40alkylene, optionally substituted C1- 30alkylene, optionally substituted C1_20alkylene, optionally tuted C4_20alkylene, optionally tuted C6_20alkylene, optionally tuted Cg_20alkylene, optionally substituted C10_20alkylene, optionally substituted C1_6alkylene, optionally substituted C2- 6alkylene, optionally substituted C3_6alkylene, optionally substituted C4_6alkylene, optionally substituted C4_5alkylene, or optionally substituted kylene.

In certain embodiments, L is an optionally substituted alkenylene, e.g., optionally substituted C2_50alkenylene, optionally substituted C2_40alkenylene, optionally substituted C2_30alkenylene, optionally substituted Cnoalkenylene, optionally substituted C4- goalkenylene, optionally substituted C6_20alkenylene, optionally substituted Cg_20all<enylene, optionally substituted C10_20alkenylene, ally substituted C2_6alkenylene, optionally substituted C3_6alkenylene, optionally substituted C4_6alkenylene, optionally tuted C4- 5alkenylene, or optionally substituted C3_4alkenylene.

In certain embodiments, L is an ally tuted alkynylene, e.g., optionally substituted C2_50alkynylene, optionally substituted C2_40alkynylene, optionally substituted lkynylene, optionally tuted Cnoalkynylene, optionally substituted C4- goalkynylene, optionally substituted C6_20alkynylene, optionally substituted Cg_20all<ynylene, optionally substituted C10_20alkynylene, optionally tuted C2_6alkynylene, optionally substituted kynylene, ally substituted kynylene, optionally tuted C4- ylene, or optionally substituted C3_4alkynylene.

In certain embodiments, L is an optionally substituted alkylene; e.g., optionally substituted heteroC1_50alkylene, optionally substituted heteroC1_40alkylene, ally tuted heteroC1_30alkylene, optionally substituted heteroC1_20alkylene, optionally substituted heteroC4_20alkylene, ally substituted C6_20alkylene, optionally substituted heterng_20all<ylene, optionally substituted C10_20alkylene, optionally substituted heteroC1_6alkylene, optionally substituted heteroC2_6alkylene, optionally substituted heteroC3_6alkylene, optionally substituted heteroC4_6alkylene, optionally substituted heteroC4_5alkylene, or optionally substituted heteroC3_4alkylene.

In n embodiments, L is an ally substituted heteroalkenylene, e.g., ally substituted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, optionally substituted heteroC2_30alkenylene, optionally substituted heteroC2_20alkenylene, optionally substituted heteroC4_20alkenylene, optionally substituted heteroC6_20alkenylene, optionally substituted heterng_20all<enylene, optionally substituted heteroC10_20alkenylene, optionally substituted heteroC2_6alkenylene, optionally substituted heteroC3_6alkenylene, optionally substituted heteroC4_6alkenylene, optionally substituted heteroC4_5alkenylene, or optionally substituted heteroC3_4alkenylene.

In certain embodiments, L is an optionally substituted alkynylene, e.g., optionally substituted heteroC2_50alkynylene, optionally substituted heteroC2_40alkynylene, optionally substituted heteroC2_30alkynylene, optionally substituted heteroC2_20alkynylene, optionally tuted heteroC4_20alkynylene, optionally substituted heteroC6_20alkynylene, optionally substituted heterng_20all<ynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, ally substituted C3_6alkynylene, optionally substituted heteroC4_6alkynylene, optionally substituted C4_5alkynylene, or optionally substituted heteroC3_4alkynylene.

In certain embodiments, L is an optionally substituted carbocyclylene, e.g., optionally substituted C340 carbocyclylene, optionally substituted C5_g carbocyclylene, optionally substituted C5_6 carbocyclylene, optionally substituted C5 carbocyclylene, or optionally substituted C6 carbocyclylene.

In certain embodiments, L is an optionally substituted cyclylene, e.g., optionally substituted 3— l4 membered heterocyclylene, optionally substituted 3—10 membered heterocyclylene, optionally substituted 5—8 membered heterocyclylene, optionally substituted —6 membered heterocyclylene, optionally substituted 5 membered heterocyclylene, or ally substituted 6 membered cyclylene.

In certain embodiments, L is an optionally substituted arylene, e.g., optionally substituted phenylene.

In certain embodiments, L is an optionally substituted heteroarylene, e.g., optionally substituted 5— l4 membered heteroarylene, optionally tuted 5—10 membered arylene, optionally substituted 5—6 membered heteroarylene, optionally substituted 5 membered heteroarylene, or optionally substituted 6 membered heteroarylene.

For example, in certain embodiments, wherein L is an optionally substituted alkylene group, the group of a (iv) is a group of the formula: n q is an integer between 1 and 50, inclusive.

In certain embodiments, q is an integer n 1 and 40, inclusive. In certain embodiments, q is an r between 1 and 30, inclusive. In certain embodiments, q is an integer between 1 and 20, inclusive. In certain embodiments, q is an integer between 4 and , inclusive. In certain embodiments, q is an integer between 6 and 20, inclusive. In certain embodiments, q is an r between 8 and 20, inclusive. In certain embodiments, q is 1. In certain embodiments, q is 2. In certain embodiments, q is 3. In certain embodiments, q is 4. In certain embodiments, q is 5. In certain embodiments, q is 6. In certain embodiments, q is 7. In certain ments, q is 8. In certain embodiments, q is 9. In n embodiments, q is 10.

In certain ments, both R6 and R7 are hydrogen. In certain embodiments, R6 is hydrogen and R7 is a group of the formula (i), (ii), or (iii). In certain embodiments, R6 is hydrogen and R7 is a group of the formula (i). In certain embodiments, R6 is hydrogen and R7 is a group of the formula (ii). In certain embodiments, R6 is hydrogen and R7 is a group of the formula (iii). In n embodiments, both R6 and R7 are ndently a group of the formula (i), (ii), or (iii). In certain embodiments, both R6 and R7 are independently a group of the formula (i). In certain embodiments, both R6 and R7 are independently a group of the a (ii). In certain embodiments, both R6 and R7 are independently a group of the formula (iii). In certain embodiments, both R6 and R7 are the same group, selected from a group of the formula (i), (ii), or (iii).

It is understood that R1 encompasses amino acid side chains such as exemplified in Table l of the Examples. In certain ments, R1 is a group selected from any one of the amino acid side chain groups listed therein.

In certain embodiments, each instance of R1 is the same. In certain embodiments, at least one R1 group is different. In certain embodiments, each R1 group is different.

As generally defined above, each instance of W is independently O, S, or NRW, wherein RW is hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii). In n embodiments, W is O.

In certain embodiments, W is S. In certain embodiments, W is NRW. In certain embodiments, RW is hydrogen or a group of the formula (i), (ii), or (iii).

] As generally defined above, each instance of Y is independently O, S, or NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group. In certain embodiments, Y is O. In certain embodiments, each instance of Y is S. In certain embodiments, Yis NRY. In n embodiments, RY is hydrogen or a nitrogen ting group.

] In n embodiments, W is O and Y is O. In certain embodiments, W is O and Y is S. In certain ments, W is O and Y is NRY. In certain embodiments, W is S and Y is O. In certain ments, W is S and Y is S. In certain embodiments, W is S and Y is NRY. In certain embodiments, W is NRW and Y is O. In certain embodiments, W is NRW and Y is S. In certain embodiments, W is NRW and Y is NRY.

As generally d above, R8 is hydrogen, a group of the formula (i), (ii), or (iii), or a group of the formula (v): wherein R2, R3, R5, Z, m, and n are as defined in Formula (I), provided at least one instance of RW, R2, 113,118,116 or R8 is a group of the formula (i), , R7, (ii), or (iii).

In certain embodiments, R8 is hydrogen.

In certain embodiments, R8 is a group of the formula (i), (ii), or (iii). In n embodiments, R8 is a group of the formula (i). In certain embodiments, R8 is a group of the a (ii). In certain embodiments, R8 is a group of the formula (iii).

] In certain embodiments, R8 is a group of the formula (V). In certain embodiments, R8 is a group of the a (V) and R2 is a group of the formula (i), (ii), or (iii). In n ments, R8 is a group of the formula (V) and R3 is a group of the formula (i), (ii), or (iii).

In certain embodiments, at least one R1 is a group of a (iv) and R6 is a group of the formula (i), (ii), or (iii). In certain embodiments, at least one R1 is a group of formula (iv) and R7 is a group of the formula (i), (ii), or (iii). In certain embodiments, at least one R1 is a group of formula (iv), and both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

Alternatively, in certain embodiments, R8 and the adjacent R1 group are joined to form an optionally substituted 5—6 membered heterocyclic ring, e.g., a 5—membered heterocyclic ring, e.g., an optionally substituted pyrrolidinyl ring.

Various combinations of the above embodiments of Formula (II) are contemplated herein.

] For example, in certain embodiments, wherein each instance of R’ is hydrogen, W is O and Y is O, the compound of Formula (II) is a compound of Formula (II—a): RS’N\ARL (II—a) or salt thereof. In certain embodiments, R8 is a group of the formula (i), (ii), or (iii). In certain embodiments, R8 is a group of the formula (V) and R2 is a group of the formula (i), (ii), or (iii). In certain embodiments, R8 is a group of the formula (V) and R3 is a group of the formula (i), (ii), or (iii). In certain embodiments, at least one R1 is a group of formula (iv). In n embodiments, R1 is a group of a (iv) and R6 is a group of the formula (i), (ii), or (iii). In certain embodiments, R1 is a group of formula (iv) and R7 is a group of the formula (i), (ii), or (iii). In certain embodiments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of a (II—a), wherein R1 alpha to the group — C(=O)—O— is a group of formula (iv), provided is a compound of Formula (II—b): 2012/062222 R7—N—LWJKFf o RS’N\ARL (II-b) or salt thereof. In certain embodiments, L is an optionally substituted ne. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In n embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In n embodiments of Formula (II—a), wherein R8 is a group of formula (V), provided is a compound of a (II—c): “ (II-c) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In certain ments, R2 is a group of formula (i). In certain embodiments, R2 is a group of a (ii). In certain embodiments, R2 is a group of formula (iii). In certain embodiments, R3 is a group of formula (i). In certain embodiments, R3 is a group of formula (ii). In certain embodiments, R3 is a group of formula (iii). In certain embodiments, R5 is hydrogen. In certain embodiments, Z is O. In certain embodiments, n is 0. In certain embodiments, n is 1.

In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5. In certain embodiments, m is 1.

In certain embodiments of Formula (II—c), wherein R1 alpha to the group — C(=O)—O— is a group of a (iV), provided is a compound of Formula ): Fr 0 R7—N—L\‘/U\O2 R3 I5 N\)\RL | N RZ—N m n (II—cl) or salt thereof. In certain embodiments, L is an optionally tuted alkylene. In certain embodiments, R6 is a group of a (i). In certain ments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain ments, R7 is a group of formula (ii). In certain ments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—c), wherein each instance of R1 provided in group R8 is a group of formula (iv), provided is a compound of Formula (II—c2): or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of formula (iii). In n embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain ments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—c), wherein each instance of R1 is a group of formula (iv), provided is a compound of Formula (II—c3): R6 o (II—c3) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of a (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In n embodiments, both R6 and R7 are ndently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—a), wherein R8 is a group of formula (i), provided is a compound of Formula (II—d): R YP /\\/N\)\RL RL (II—d) or salt thereof. In certain embodiments, R1 is hydrogen. In certain embodiments, R1 is a group of formula (iv). In certain embodiments, R1 is a group of formula (iv) and R6 is a group of the formula (i), (ii), or (iii). In certain embodiments, R1 is a group of formula (iv) and both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

] In certain embodiments of Formula , wherein R1 alpha to the group — C(=O)—O— is a group of a (iv), provided is a compound of Formula (II—dl): RL (II—d1) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of a (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain ments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—a), wherein R8 is a group of formula (ii), provided is a compound of Formula (II—e): O (II—e) or salt thereof. In certain embodiments, R1 is hydrogen. In certain embodiments, R1 is a group of formula (iv). In n embodiments, R1 is a group of a (iv) and R6 is a group of the formula (i), (ii), or (iii). In certain embodiments, R1 is a group of formula (iv) and both R6 and R7 are independently groups of the formula (i), (ii), or (iii). 2012/062222 In certain embodiments of Formula (II—e), wherein R1 alpha to the group — C(=O)—O— is a group of formula (iv), provided is a compound of Formula (II—el): R6 o R —N—L7 \ARL O (II-el) or salt thereof. In certain embodiments, L is an ally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In n embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of a (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of a (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—a), wherein R8 is a group of formula (iii), provided is a compound of Formula : RLVN\ARL (II-f) or salt thereof. In n embodiments, R1 is hydrogen. In certain ments, R1 is a group of formula (iv). In certain embodiments, R1 is a group of formula (iv) and R6 is a group of the formula (i), (ii), or (iii). In certain ments, R1 is a group of formula (iv) and both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—f), n R1 alpha to the group — C(=O)—O— is a group of formula (iv), provided is a compound of Formula (II—fl): R6 o R7—rlJ—L\Hko RVNL \ARL (II—f1) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of the formula (i), (ii), or (iii).

In certain embodiments of Formula (II—a), n R1 and R8 are joined to form an optionally substituted 5—6 membered heterocyclic ring, provided is a nd of Formula (11—g): KARL (II-g) or salt thereof. In certain embodiments, L is an optionally substituted alkylene.

Compounds ofFormula (111) Compounds of Formula (111) are the cyclic condensation product of the same or different two, three, four, five, siX, seven, eight, nine, or ten amino acids, and which further se one or more sites of conjugation attached thereto, e.g., to an internal amide nitrogen, to an amino tuent, and/or to an imino nitrogen, of a group of formula (i), (iii), or (iii). Such groups may be conjugated before cyclization, i.e., to the amino acid precursors of the cyclization product, or after cyclization. internal amide nitrogens amino substituents imino nitrogens Thus, in a third aspect, provided is a compound of Formula (111): or salt thereof; wherein: p is an integer of n 1 and 9, inclusive; each instance of Q is independently O, S, or NRQ, wherein RQ is en, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), (iii); each instance of R1 is independently en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1; wherein each occurrence of RAl is independently hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, ally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when ed to an oxygen atom, a sulfur protecting group when attached to an sulfur atom, a nitrogen protecting group when attached to a nitrogen atom, or two RAl groups are joined to form an optionally substituted heterocyclic or optionally substituted heteroaryl ring; and each instance of R2 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen ting group, or a group of the formula (i), (ii), or (iii); and Formulae (i), (ii), and (iii) are: RLB—YRP H\ RL RI :4 (1) (ii) (iii) each instance of R’ is independently hydrogen or optionally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, wherein RY is en, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 l, optionally substituted C250 alkynyl, optionally tuted C1_50 alkyl, optionally tuted heteroC2_50 l, optionally substituted C2_50 alkynyl, or a polymer; provided that at least one instance of RQ, R2, R6, or R7 is a group of the formula (i), (ii), or (iii).

As generally defined above, p is an integer of between 1 and 9, inclusive. In certain embodiments, p is 1. In certain embodiments, p is 2. In n embodiments, p is 3. In certain embodiments, p is 4. In certain embodiments, p is 5. In certain embodiments, p is 6.

In certain embodiments, p is 7. In certain embodiments, p is 8. In certain ments, p is For example, in certain embodiments, wherein p is l, the compound of Formula (III) is a compound of Formula (III—a): R2 R1 0&0\N R1 R2 (III—a) or salt thereof.

In certain embodiments, wherein p is 2, the compound of Formula (III) is a compound of a (III—b): RRZ/Nfi Q (III-b) or salt thereof.

In certain embodiments, wherein p is 3, the compound of Formula (III) is a compound of Formula (III—c): R2 R1 ) or salt thereof.

In certain embodiments, wherein p is 4, the compound of Formula (III) is a compound of Formula (III—d): Q R1 RVkILJYQR2 R2 Q R (III-d) or salt thereof.

In certain embodiments, wherein p is 5, the compound of Formula (III) is a compound of Formula (III—e): Q R1 RKkaJYQ Q R1 Rj:N’R2 $2 l:oN\R2 R2 Rz,N QA/Nfiw R1 0 (III—e) or salt thereof.

In certain embodiments, n p is 6, the compound of Formula (III) is a compound of Formula (III—f): WO 63468 Q (III-f) or salt f.

In certain embodiments, wherein p is 7, the compound of Formula (111) is a compound of Formula (III—g): 1 Q Q R1 R1 N\ IN Q R2 R2 R1QjN\R2N/R2 R2RZ’NZW\ Q R2 2 R1 a Q Q R1 (111-g) or salt thereof.

In certain embodiments, wherein p is 8, the compound of Formula (111) is a compound of Formula (III—h): R1 R2 (III—h) or salt thereof.

In certain embodiments, wherein p is 9, the compound of Formula (III) is a compound of Formula (III—i): QR1RZQR1 RVfNJYlfideJYQ or salt f.

As generally defined above, each ce of R’ is independently hydrogen or optionally tuted alkyl. In certain embodiments, at least one instance of R’ is hydrogen.

In certain embodiments, at least two instances of R’ is hydrogen. In certain embodiments, each instance of R’ is hydrogen. In certain embodiments, at least one instance of R’ is optionally substituted alkyl, e.g., methyl. In certain embodiments, at least two instances of R’ is optionally substituted alkyl, e.g., methyl. In certain embodiments, one ce of R’ is optionally substituted alkyl, and the rest are hydrogen.

As generally defined above, each instance of Q is ndently O, S, or NRQ, wherein RQ is hydrogen, ally tuted alkyl, optionally tuted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen ting group, or a group of the formula (i), (ii), or (iii). In certain embodiments, at least one instance of Q is O. In certain embodiments, each instance of Q is O. In certain embodiments, at least one instance of Q is S. In certain embodiments, each instance of Q is S. In certain embodiments, at least one instance of Q is NRZ. In certain embodiments, each instance of Q is NRZ. In certain embodiments, each instance of RQ is independently hydrogen or a group of the formula (i), (ii), or (iii).

As generally defined above, each instance of R1 is independently hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1.

In certain embodiments, at least one instance of R1 is ally substituted alkyl, optionally substituted l, optionally tuted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or ally substituted heteroaryl.

] In certain embodiments, at least one instance of R1 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally tuted C2_6alkyl, optionally substituted C3_6alkyl, optionally substituted C4_6alkyl, optionally tuted kyl, or optionally substituted C34alkyl.

In certain embodiments, at least one instance of R1 is optionally substituted alkenyl, e.g., optionally tuted C2_6alkenyl, optionally tuted C3_6alkenyl, optionally substituted C4_6alkenyl, optionally substituted C4_5alkenyl, or ally substituted C3- 4alkenyl.

In certain embodiments, at least one instance of R1 is optionally substituted alkynyl, e.g., optionally substituted C2_6alkynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally tuted C3- 4alkynyl.

In certain embodiments, at least one instance of R1 is optionally substituted carbocyclyl, e.g., optionally substituted C3_10 carbocyclyl, optionally substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally substituted C6 carbocyclyl.

In certain embodiments, at least one ce of R1 is optionally substituted heterocyclyl, e.g., optionally substituted 3—14 membered heterocyclyl, optionally substituted 3—10 membered heterocyclyl, optionally substituted 5—8 membered heterocyclyl, optionally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In certain embodiments, at least one instance of R1 is ally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, at least one instance of R1 is optionally substituted heteroaryl, e.g., optionally substituted 5—14 membered heteroaryl, optionally substituted 5—10 membered aryl, optionally substituted 5—6 ed heteroaryl, optionally substituted membered heteroaryl, or optionally substituted 6 ed heteroaryl.

In any of the above embodiments, the R1 alkyl, alkenyl, alkynyl, yclyl, heterocyclyl, aryl, or heteroaryl group may be substituted, for example, with an optionally tuted amino group (e.g., —NR6R7), an ally substituted hydroxyl group (e.g., —OR6), an optionally tuted thiol group (e.g., —SR6), or with a group of formula (i), (ii), or (iii), wherein each instance of R6 and R7 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted aryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or a group of formula (i), (ii), or (iii).

For e, in certain embodiments, at least one instance of R1 is an alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or aryl group tuted with an amino group of the a —N(R6)(R7). In that instance, in certain embodiments, at least one instance of R1 is a group of formula: wherein: L is an optionally substituted alkylene, optionally substituted alkenylene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, or optionally substituted heteroarylene, or combination thereof, and R6 and R7 are independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally tuted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, and a nitrogen protecting group; ed at least one instance of R6 and R7 is a group of the a (i), (ii), or (iii): R‘ XRL RQ—YRP §—§RI § 0 R'- R. or g_/ (i) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In certain embodiments, at least two ces of R1 is a group of formula (iv).

In certain embodiments, at least three instances of R1 is a group of formula (iv). In certain ments, at least four instances of R1 is a group of formula (iv). In certain embodiments, at least five instances of R1 is a group of formula (iv). In certain embodiments, at least six instances of R1 is a group of formula (iv). In certain embodiments, at least seven instances of R1 is a group of formula (iv). In certain embodiments, at least eight instances of R1 is a group of formula (iV). In n embodiments, at least nine instances of R1 is a group of formula (iv). In certain embodiments, each instance of R1 is a group of formula (iv).

In certain embodiments, L is an optionally substituted alkylene; e.g., ally substituted C1_50alkylene, ally substituted C1_40alkylene, optionally substituted C1- 30alkylene, optionally substituted C1_20alkylene, optionally substituted C4_20alkylene, optionally tuted C6_20alkylene, optionally substituted Cg_20all<ylene, optionally substituted C10_20alkylene, optionally substituted C1_6alkylene, optionally substituted C2- 6alkylene, optionally substituted C3_6alkylene, optionally substituted kylene, optionally substituted C4_5alkylene, or optionally substituted C3_4alkylene.

In certain embodiments, L is an optionally substituted alkenylene, e.g., optionally substituted C2_50alkenylene, optionally substituted C2_40alkenylene, optionally substituted C2_30alkenylene, optionally substituted Cnoalkenylene, optionally substituted C4- goalkenylene, optionally substituted C6_20alkenylene, optionally tuted Cg_20all<enylene, optionally substituted C10_20alkenylene, optionally substituted C2_6alkenylene, optionally substituted C3_6alkenylene, optionally substituted kenylene, optionally substituted C4- ylene, or ally tuted C3_4alkenylene.

In certain embodiments, L is an optionally substituted alkynylene, e.g., optionally tuted C2_50alkynylene, optionally substituted C2_40alkynylene, optionally substituted C2_30alkynylene, ally substituted Cnoalkynylene, optionally substituted C4- goalkynylene, optionally substituted C6_20alkynylene, ally substituted Cg_20all<ynylene, optionally substituted alkynylene, optionally substituted C2_6alkynylene, ally substituted C3_6alkynylene, optionally substituted C4_6alkynylene, optionally tuted C4- 5alkynylene, or optionally substituted C3_4alkynylene.

In certain embodiments, L is an optionally substituted heteroalkylene; e.g., optionally substituted heteroC1_50alkylene, optionally substituted C1_40alkylene, optionally substituted heteroC1_30alkylene, optionally substituted heteroC1_20alkylene, optionally substituted heteroC4_20alkylene, optionally substituted heteroC6_20alkylene, optionally substituted heterng_20all<ylene, optionally substituted heteroC10_20alkylene, optionally substituted heteroC1_6alkylene, optionally substituted heteroC2_6alkylene, optionally substituted heteroC3_6alkylene, optionally tuted heteroC4_6alkylene, optionally substituted heteroC4_5alkylene, or optionally tuted heteroC3_4alkylene.

In certain embodiments, L is an optionally substituted heteroalkenylene, e.g., optionally substituted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, ally substituted heteroC2_30alkenylene, optionally substituted heteroC2_20alkenylene, optionally substituted heteroC4_20alkenylene, ally substituted heteroC6_20alkenylene, optionally substituted heterng_20all<enylene, optionally substituted heteroC10_20alkenylene, optionally substituted heteroC2_6alkenylene, optionally substituted heteroC3_6alkenylene, ally substituted heteroC4_6alkenylene, optionally substituted heteroC4_5alkenylene, or optionally substituted heteroC3_4alkenylene.

In certain embodiments, L is an optionally substituted heteroalkynylene, e.g., optionally substituted heteroC2_50alkynylene, optionally substituted heteroC2_40alkynylene, ally substituted heteroC2_30alkynylene, optionally substituted C2_20all<ynylene, optionally substituted heteroC4_20alkynylene, optionally substituted heteroC6_20alkynylene, optionally substituted g_20all<ynylene, optionally substituted heteroC10_20alkynylene, optionally tuted heteroC2_6alkynylene, optionally tuted heteroC3_6alkynylene, optionally tuted heteroC4_6alkynylene, optionally substituted heteroC4_5alkynylene, or optionally tuted heteroC3_4alkynylene.

In certain embodiments, L is an optionally substituted carbocyclylene, e.g., optionally substituted C340 carbocyclylene, optionally substituted C5_g carbocyclylene, optionally substituted C5_6 carbocyclylene, optionally substituted C5 carbocyclylene, or optionally substituted C6 carbocyclylene.

In certain embodiments, L is an optionally substituted cyclylene, e.g., optionally substituted 3— l4 membered heterocyclylene, optionally substituted 3—10 ed heterocyclylene, optionally substituted 5—8 ed heterocyclylene, optionally substituted —6 membered cyclylene, optionally substituted 5 membered heterocyclylene, or optionally substituted 6 membered heterocyclylene.

] In certain embodiments, L is an optionally substituted arylene, e.g., optionally substituted phenylene.

In certain embodiments, L is an ally substituted heteroarylene, e.g., optionally substituted 5— l4 membered arylene, optionally substituted 5—10 membered heteroarylene, ally substituted 5—6 membered heteroarylene, optionally substituted 5 membered heteroarylene, or optionally substituted 6 membered heteroarylene.

For example, in certain embodiments, wherein L is an optionally substituted alkylene group, the group of formula (iV) is a group of the formula: Ir"\9;N wherein q is an integer between 1 and 50, inclusive.

In certain embodiments, q is an integer between 1 and 40, inclusive. In certain embodiments, q is an integer between 1 and 30, inclusive. In certain embodiments, q is an integer between 1 and 20, inclusive. In certain embodiments, q is an integer between 4 and , inclusive. In certain embodiments, q is an integer between 6 and 20, ive. In n embodiments, q is an integer between 8 and 20, inclusive. In certain embodiments, q is 1. In certain embodiments, q is 2. In certain embodiments, q is 3. In certain embodiments, q is 4. In certain embodiments, q is 5. In certain embodiments, q is 6. In certain embodiments, q is 7. In certain ments, q is 8. In certain embodiments, q is 9. In certain embodiments, q is 10.

In certain embodiments, both R6 and R7 are hydrogen. In certain embodiments, R6 is hydrogen and R7 is a group of the formula (i), (ii), or (iii). In certain embodiments, R6 is hydrogen and R7 is a group of the formula (i). In certain embodiments, R6 is hydrogen and R7 is a group of the a (ii). In certain embodiments, R6 is hydrogen and R7 is a group of the formula (iii). In certain embodiments, both R6 and R7 are ndently a group of the a (i), (ii), or (iii). In certain embodiments, both R6 and R7 are independently a group of the formula (i). In certain embodiments, both R6 and R7 are independently a group of the formula (ii). In certain embodiments, both R6 and R7 are independently a group of the formula (iii). In certain embodiments, both R6 and R7 are the same group, ed from a group of the formula (i), (ii), or (iii).

It is tood that R1 encompasses amino acid side chains such as exemplified in Table l of the Examples. In n embodiments, R1 is a group selected from any one of the amino acid side chain groups listed therein.

In certain embodiments, each instance of R1 is the same. In certain ments, at least one R1 group is different. In certain embodiments, each R1 group is different.

As generally defined above, each instance of R2 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally tuted alkynyl, optionally substituted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii): . Fa' )(FRL H; o R, 01' §_/RL (i) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In certain embodiments, at least one instance of R2 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally substituted C2_6alkyl, optionally substituted kyl, optionally tuted C4_6alkyl, optionally substituted C4_5alkyl, or optionally substituted yl.

In certain ments, at least one instance of R2 is ally substituted alkenyl, e.g., optionally substituted C2_6alkenyl, optionally substituted C3_6alkenyl, optionally substituted C4_6alkenyl, optionally substituted C4_5alkenyl, or optionally substituted C3- 4alkenyl.

In certain embodiments, at least one instance of R2 is optionally substituted alkynyl, e.g., optionally substituted C2_6alkynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally substituted C3- 4alkynyl.

In certain embodiments, at least one instance of R2 is optionally substituted carbocyclyl, e.g., ally substituted C3_10 carbocyclyl, optionally substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally substituted C6 carbocyclyl.

In certain embodiments, at least one instance of R2 is optionally substituted heterocyclyl, e.g., optionally substituted 3—14 membered heterocyclyl, optionally substituted 3—10 ed heterocyclyl, optionally substituted 5—8 membered heterocyclyl, optionally substituted 5—6 membered cyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In certain embodiments, at least one instance of R2 is ally tuted aryl, e.g., ally substituted phenyl.

In n embodiments, at least one instance of R2 is optionally substituted heteroaryl, e.g., optionally substituted 5—14 ed heteroaryl, optionally substituted 5—10 membered heteroaryl, optionally substituted 5—6 membered heteroaryl, optionally tuted membered heteroaryl, or optionally tuted 6 membered heteroaryl.

In certain embodiments, at least one ce of R2 is a nitrogen protecting group.

In certain embodiments, at least one instance of R2 is a group of the formula (i).

In n ments, at least one instance of R2 is a group of the formula (ii). In certain embodiments, at least one instance of R2 is a group of the formula (iii).

In certain embodiments, each instance of R2 is a group other than formula (i), (ii), or (iii); in that instance, it follows that at least one RQ is a group of the formula (i), (ii), or (iii), or at least one R1 is a group of formula (iv), and at least one of R6 or R7 encompassed by R1 is a group of the formula (i), (ii), or (iii). For example, in certain embodiments, both instances of R2 are hydrogen, and thus at least one RQ is a group of the formula (i), (ii), or (iii), or at least one R1 is a group of formula (iv), and at least one of R6 or R7 encompassed by R1 is a group of the a (i), (ii), or (iii).

Various combinations of the above embodiments of Formula (III) are contemplated herein.

For e, in certain embodiments, wherein each instance of Q is O, the compound of Formula (III) is a compound of Formula (III—a): or salt thereof. In certain embodiments, at least one R1 is a group of formula (iv). In certain embodiments, each ce of R1 is a group of formula (iv). In certain ments, each instance of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of a (ii). In certain ments, at least one instance of R2 is a group of formula (iii). In certain embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3.

In certain embodiments of Formula (III—a), wherein at least one R1 is a group the formula (iv), provided is a compound of Formula (III—b): (III-b) or salt thereof. In certain embodiments, each ce of R1 is a group of formula (iv). In certain ments, R2 is hydrogen. In certain embodiments, each instance of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of formula (ii). In certain embodiments, at least one instance of R2 is a group of formula (iii). In certain embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of a (i). In n embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of a (i), (ii), or (iii).

In n embodiments of Formula (III—a), wherein each instance of R1 is a group the formula (iV), provided is a compound of Formula (III—c): (III-c) or salt thereof. In certain embodiments, each instance of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of formula (ii). In n ments, at least one instance of R2 is a group of formula (iii). In certain embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3. In certain ments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of a (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

In certain embodiments of Formula ), wherein p is 1, provided is a compound of Formula (III—cl): Riff/R7 R7 (III-cl) or salt f. In certain embodiments, each ce of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of formula (ii). In certain embodiments, at least one instance of R2 is a group of formula (iii). In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In n embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

In certain embodiments of Formula (III—cl), wherein each instance of R2 is en, provided is a compound of Formula (III—c2): R6\N,R7 R§N_L 0:31HN—$:o 6 NH R7 (III-c2) or salt thereof. In certain embodiments, L is an optionally substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In n ments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In n embodiments, R7 is a group of formula (iii). In n embodiments, both R6 and R7 are groups of formula (i), (ii), or (iii).

In certain embodiments of Formula (III—cl), wherein L is an optionally substituted alkylene, provided is a compound of Formula (III—c3): o o R\6 NH IN q R7 (III-c3) or salt thereof, wherein q is an integer n 1 and 10, inclusive. In n embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of a (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

In certain embodiments of Formula (III—a), n at least one instance of R2 is a group of formula (i) and each instance of R’ is hydrogen, provided is a compound of Formula ): p (III-d) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iv). In certain embodiments, each instance of R1 is a group of formula (iv). In certain embodiments, each instance of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of a (ii). In certain embodiments, at least one instance of R2 is a group of formula (iii). In certain embodiments, R2 is a group of formula (iii). In certain embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3.

] In certain embodiments of a (III—a), wherein at least one instance of R2 is a group of a (ii) and each instance of R’ is hydrogen, provided is a compound of Formula ): p (III-e) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iv). In certain embodiments, each instance of R1 is a group of formula (iv). In certain ments, each instance of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one ce of R2 is a group of formula (ii). In certain embodiments, at least one instance of R2 is a group of formula (iii). In certain embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3.

In certain embodiments of Formula (III—a), wherein at least one instance of R2 is a group of formula (iii), provided is a compound of Formula (III—f): or salt thereof. In certain embodiments, at least one R1 is a group of formula (iv). In certain embodiments, each instance of R1 is a group of a (iv). In n embodiments, each instance of R2 is hydrogen. In certain embodiments, at least one instance of R2 is a group of a (i). In certain embodiments, at least one instance of R2 is a group of formula (ii). In certain embodiments, at least one instance of R2 is a group of a (iii). In n embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3. nds ofFormula (IV), (V), and (V1) Compounds of Formula (IV), (V), and (VI), while not constructed from amino acid starting materials, share the same molecular formula and cyclic motif, and are thus structural isomers of compounds of Formula (III—a). The present invention embraces each as exemplary APPL structural isomers of the t invention. ng:§=Q=_W—2—:g:QR1—<::(:E—R1R2_:;N:l§:jwR2 R1 R1 \R2 (III—a) (IV) (V1) Thus, in yet another aspect, provided is a compound of Formula (IV), (V), or Q} R1jgi§1§£§ (V1) or salt thereof; wherein: each instance of Q is independently O, S, or NRQ, wherein RQ is hydrogen, ally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, ally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of formula (i), (ii), (iii); each ce of R1 is independently hydrogen, ally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1; wherein each occurrence of RAl is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur ting group when attached to an sulfur atom, a nitrogen ting group when attached to a nitrogen atom, or two RAl groups are joined to form an optionally substituted heterocyclic or ally substituted heteroaryl ring; each instance of R2 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally substituted heteroaryl, a nitrogen protecting group, or a group of formula (i), (ii), or (iii); and Formulae (i), (ii), and (iii) are: RLB—YRP H\ RL RI :4 (1) (ii) (iii) wherein: each instance of R’ is ndently hydrogen or ally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted heterocyclyl, optionally substituted aryl, optionally substituted aryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally substituted C2_50 alkenyl, optionally substituted heteroC2_50 alkynyl, or a polymer; provided that at least one instance of RQ, R2, R6, or R7 is a group of the formula (i), (ii), or (iii).

As generally defined above, each instance of Q is independently O, S, or NRQ, wherein RQ is hydrogen, ally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii). In certain embodiments, at least one instance of Q is O. In certain embodiments, each ce of Q is O. In certain embodiments, at least one instance of Q is S. In certain embodiments, each ce of Q is S. In certain embodiments, at least one instance of Q is NRZ. In certain ments, each ce of Q is NRZ. In certain embodiments, each instance of RQ is independently hydrogen or a group of the formula (i), (ii), or (iii).

As generally defined above, each instance of R’ is independently hydrogen or optionally substituted alkyl. In certain ments, at least one instance of R’ is hydrogen.

In certain ments, at least two instances of R’ is hydrogen. In certain embodiments, each instance of R’ is hydrogen. In certain embodiments, at least one instance of R’ is optionally substituted alkyl, e.g., . In certain embodiments, at least two instances of R’ is optionally tuted alkyl, e.g., methyl. In certain embodiments, one instance of R’ is optionally substituted alkyl, and the rest are hydrogen.

As generally defined above, each instance of R1 is independently hydrogen, optionally tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1.

In n embodiments, at least one instance of R1 is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

In certain embodiments, at least one instance of R1 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally substituted C2_6alkyl, optionally substituted C3_6alkyl, optionally substituted C4_6alkyl, optionally tuted C4_5alkyl, or optionally substituted C34alkyl.

In n embodiments, at least one instance of R1 is optionally substituted alkenyl, e.g., optionally substituted C2_6alkenyl, optionally tuted C3_6alkenyl, optionally substituted C4_6alkenyl, optionally substituted kenyl, or optionally substituted C3- 4alkenyl.

In certain ments, at least one instance of R1 is optionally substituted alkynyl, e.g., ally tuted kynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally substituted C3- 4alkynyl.

In certain embodiments, at least one instance of R1 is optionally substituted carbocyclyl, e.g., optionally substituted C3_10 carbocyclyl, optionally tuted C5_g carbocyclyl, optionally tuted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally substituted C6 yclyl.

In certain embodiments, at least one instance of R1 is optionally substituted heterocyclyl, e.g., optionally substituted 3—14 membered heterocyclyl, optionally substituted 3—10 membered heterocyclyl, optionally substituted 5—8 ed heterocyclyl, optionally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In certain embodiments, at least one ce of R1 is optionally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, at least one ce of R1 is optionally substituted heteroaryl, e.g., optionally tuted 5—14 membered heteroaryl, optionally substituted 5—10 membered heteroaryl, optionally substituted 5—6 membered heteroaryl, ally substituted membered heteroaryl, or optionally substituted 6 membered heteroaryl.

In any of the above embodiments, the R1 alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl group may be substituted, for example, with an optionally substituted amino group (e.g., —NR6R7), an optionally substituted hydroxyl group (e.g., —OR6), an optionally substituted thiol group (e.g., —SR6), or with a group of formula (i), (ii), or (iii), wherein each ce of R6 and R7 is independently en, optionally substituted alkyl, optionally tuted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally tuted aryl, a en protecting group when attached to a en atom, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or a group of formula (i), (ii), or (iii).

For example, in certain embodiments, at least one instance of R1 is an alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl group substituted with an amino group of the formula —N(R6)(R7). In that instance, in certain embodiments, at least one ce of R1 is a group of a: wherein: L is an optionally substituted alkylene, optionally substituted alkenylene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, or optionally substituted heteroarylene, or combination thereof, and R6 and R7 are independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, ally substituted alkynyl, ally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, and a nitrogen ting group; provided at least one instance of R6 and R7 is a group of the formula (i), (ii), or (iii): é—flR.\ RL (1) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In n embodiments, both instances of R1 are groups of formula (iv).

In certain embodiments, L is an optionally substituted alkylene; e.g., optionally substituted C1_50alkylene, optionally substituted C1_40alkylene, optionally substituted C1- 30alkylene, optionally substituted C1_20alkylene, optionally substituted C4_20alkylene, optionally substituted C6_20alkylene, optionally substituted Cg_20all<ylene, optionally substituted C10_20alkylene, optionally substituted C1_6alkylene, optionally substituted C2- 6alkylene, optionally substituted C3_6alkylene, ally tuted C4_6alkylene, optionally substituted C4_5alkylene, or optionally substituted C3_4alkylene.

In n embodiments, L is an optionally substituted lene, e.g., optionally substituted C2_50alkenylene, ally substituted C2_40alkenylene, optionally substituted C2_30alkenylene, optionally substituted C2_20alkenylene, optionally substituted C4- goalkenylene, optionally tuted C6_20alkenylene, optionally substituted Cg_20all<enylene, optionally substituted alkenylene, optionally substituted C2_6alkenylene, optionally substituted C3_6alkenylene, optionally substituted C4_6alkenylene, optionally tuted C4- 5alkenylene, or optionally tuted C3_4alkenylene.

] In certain embodiments, L is an optionally substituted alkynylene, e.g., optionally substituted C2_50alkynylene, optionally substituted C2_40alkynylene, optionally substituted C2_30alkynylene, optionally substituted ynylene, optionally substituted C4- goalkynylene, optionally substituted C6_20alkynylene, optionally substituted ll<ynylene, optionally tuted C10_20alkynylene, optionally substituted C2_6alkynylene, optionally substituted C3_6alkynylene, optionally substituted C4_6alkynylene, optionally substituted C4- 5alkynylene, or ally substituted C3_4alkynylene.

In certain embodiments, L is an optionally substituted heteroalkylene; e.g., optionally substituted heteroC1_50alkylene, optionally substituted heteroC1_40alkylene, ally substituted heteroC1_30alkylene, optionally substituted heteroC1_20alkylene, ally substituted heteroC4_20alkylene, optionally substituted heteroC6_20alkylene, optionally substituted heterng_20all<ylene, optionally substituted heteroC10_20alkylene, optionally substituted heteroC1_6alkylene, optionally substituted heteroC2_6alkylene, optionally substituted heteroC3_6alkylene, optionally substituted heteroC4_6alkylene, optionally substituted heteroC4_5alkylene, or optionally substituted heteroC3_4alkylene.

In certain embodiments, L is an optionally substituted heteroalkenylene, e.g., optionally substituted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, optionally substituted heteroC2_30alkenylene, optionally substituted C2_20all<enylene, optionally substituted heteroC4_20alkenylene, optionally tuted heteroC6_20alkenylene, optionally substituted heterng_20alkenylene, optionally substituted heteroC10_20alkenylene, optionally substituted heteroC2_6alkenylene, optionally substituted heteroC3_6alkenylene, optionally substituted heteroC4_6alkenylene, optionally substituted heteroC4_5alkenylene, or ally substituted heteroC3_4alkenylene.

In certain embodiments, L is an optionally substituted heteroalkynylene, e.g., optionally substituted heteroC2_50alkynylene, optionally tuted heteroC2_40alkynylene, optionally substituted heteroC2_30alkynylene, optionally substituted heteroC2_20alkynylene, ally substituted heteroC4_20alkynylene, ally substituted heteroC6_20alkynylene, optionally substituted heterng_20all<ynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, optionally substituted C3_6alkynylene, optionally tuted heteroC4_6alkynylene, ally substituted heteroC4_5alkynylene, or optionally tuted heteroC3_4alkynylene.

In certain embodiments, L is an optionally tuted carbocyclylene, e.g., optionally substituted C340 carbocyclylene, optionally substituted C5_g carbocyclylene, optionally substituted C5_6 carbocyclylene, optionally substituted C5 carbocyclylene, or optionally substituted C6 carbocyclylene.

In certain embodiments, L is an optionally substituted heterocyclylene, e.g., optionally substituted 3— l4 membered heterocyclylene, optionally substituted 3—10 ed heterocyclylene, optionally substituted 5—8 membered heterocyclylene, optionally substituted —6 membered cyclylene, optionally tuted 5 membered heterocyclylene, or optionally substituted 6 membered heterocyclylene.

In certain embodiments, L is an optionally substituted e, e.g., optionally substituted phenylene.

In certain ments, L is an optionally substituted heteroarylene, e.g., optionally substituted 5— l4 membered heteroarylene, optionally substituted 5—10 membered heteroarylene, optionally substituted 5—6 membered heteroarylene, optionally substituted 5 ed heteroarylene, or ally substituted 6 membered heteroarylene.

For example, in certain embodiments, wherein L is an optionally tuted alkylene group, the group of formula (iv) is a group of the formula: wherein q is an integer between 1 and 50, inclusive.

In certain embodiments, q is an integer between 1 and 40, inclusive. In certain embodiments, q is an integer between 1 and 30, inclusive. In certain embodiments, q is an integer between 1 and 20, inclusive. In certain embodiments, q is an integer between 4 and , ive. In certain embodiments, q is an integer between 6 and 20, inclusive. In certain embodiments, q is an integer between 8 and 20, inclusive. In certain embodiments, q is 1. In certain embodiments, q is 2. In certain embodiments, q is 3. In certain embodiments, q is 4. In n embodiments, q is 5. In certain embodiments, q is 6. In certain embodiments, q is 7. In certain embodiments, q is 8. In certain embodiments, q is 9. In certain embodiments, q is 10.

] In certain embodiments, both R6 and R7 are hydrogen. In certain embodiments, R6 is hydrogen and R7 is a group of the formula (i), (ii), or (iii). In certain embodiments, R6 is hydrogen and R7 is a group of the a (i). In certain embodiments, R6 is hydrogen and R7 is a group of the a (ii). In certain embodiments, R6 is hydrogen and R7 is a group of the formula (iii). In certain embodiments, both R6 and R7 are independently a group of the formula (i), (ii), or (iii). In certain embodiments, both R6 and R7 are independently a group of the formula (i). In certain embodiments, both R6 and R7 are independently a group of the formula (ii). In certain embodiments, both R6 and R7 are independently a group of the formula (iii). In certain embodiments, both R6 and R7 are the same group, selected from a group of the formula (i), (ii), or (iii).

It is understood that R1 encompasses amino acid side chains such as exemplified in Table l of the Examples. In certain embodiments, R1 is a group ed from any one of the amino acid side chain groups listed therein.

In n embodiments, each instance of R1 is the same. In certain embodiments, at least one R1 group is different. In certain embodiments, each R1 group is different.

As lly defined above, each instance of R2 is independently en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii): é—flR.\ RL (1) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In certain embodiments, at least one instance of R2 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally substituted C2_6alkyl, optionally substituted C3_6alkyl, optionally substituted kyl, ally tuted C4_5alkyl, or optionally substituted C34alkyl.

In n ments, at least one instance of R2 is ally substituted alkenyl, e.g., optionally substituted C2_6alkenyl, optionally substituted C3_6alkenyl, optionally substituted C4_6alkenyl, optionally substituted C4_5alkenyl, or optionally substituted C3- In certain embodiments, at least one instance of R2 is optionally substituted alkynyl, e.g., optionally substituted C2_6alkynyl, optionally substituted C3_6alkynyl, ally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or optionally substituted C3- 4alkynyl.

In n embodiments, at least one instance of R2 is ally substituted yclyl, e.g., optionally substituted C3_10 carbocyclyl, optionally substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, ally substituted C5 carbocyclyl, or optionally substituted C6 carbocyclyl.

In certain embodiments, at least one instance of R2 is optionally substituted heterocyclyl, e.g., optionally substituted 3—14 ed heterocyclyl, optionally substituted 3—10 membered heterocyclyl, optionally substituted 5—8 ed heterocyclyl, optionally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 membered heterocyclyl.

In certain embodiments, at least one instance of R2 is optionally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, at least one instance of R2 is optionally substituted heteroaryl, e.g., optionally substituted 5—14 ed heteroaryl, optionally substituted 5—10 membered heteroaryl, ally substituted 5—6 membered heteroaryl, optionally substituted membered heteroaryl, or optionally substituted 6 membered heteroaryl.

In certain embodiments, at least one instance of R2 is a nitrogen protecting group.

In certain embodiments, at least one instance of R2 is a group of the formula (i).

In certain embodiments, at least one instance of R2 is a group of the formula (ii). In certain embodiments, at least one instance of R2 is a group of the formula (iii).

] In certain embodiments, each ce of R2 is a group other than formula (i), (ii), or (iii); in that instance, it follows that at least one RQ is a group of the formula (i), (ii), or (iii), or at least one R1 is a group of formula (iV), and at least one of R6 or R7 encompassed by R1 is a group of the formula (i), (ii), or (iii). For example, in certain embodiments, both instances of R2 are hydrogen, and thus at least one RQ is a group of the formula (i), (ii), or 2012/062222 (iii), or at least one R1 is a group of formula (iv), and at least one of R6 or R7 encompassed by R1 is a group of the formula (i), (ii), or (iii).

Various ations of the above embodiments of Formula (IV), (V), and (VI) are contemplated herein. For example, in certain embodiments, wherein each instance of Q is O, the compound of Formula (IV), (V), or (VI) is a compound of Formula (IV—a), (V—a), or {i} 1:1i1fii1 R(—IVa)0 (V—a)0 )R or salt thereof. In n embodiments, at least one instance of R1 is a group of formula (iv).

In certain embodiments, each ce of R1 is a group of formula (iv). In certain embodiments, at least one instance of R2 is optionally substituted alkyl, optionally substituted alkenyl, or optionally substituted alkynyl. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain ments, at least one instance of R2 is a group of formula (ii). In certain embodiments, at least one instance of R2 is a group of formula (iii).

] In certain embodiments of Formula (IV—a), (V—a), or (VI—a), wherein at least one R1 is a group the formula (iv), provided is a compound of Formula (IV—b), (V—b), or (VI—b): R5—N: Rig} R7 R21): £4? R7 R2 O:R6—N (IV—b) (V-b) (VI-b) or salt thereof. In certain embodiments, at least one instance of R2 is optionally substituted alkyl, optionally substituted alkenyl, or optionally substituted alkynyl. In certain embodiments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of a (ii). In certain embodiments, at least one instance of R2 is a group of a (iii). In certain embodiments, L is an optionally tuted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of a (iii). In certain embodiments, R7 is a group of a (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii). 2012/062222 In certain embodiments of Formula (IV—b), (V—b), or (VI—b), wherein both R1 groups are a group the formula (iv), provided is a compound of a (IV—c), (V—c), or (VI—c): R\6 R\2 o N—R7 R2 0 /N L/ /R2 ‘N R2— L N L L IN_R7 L o Re—N/ N N—R7 o L R5 / \ ’ é / REL—N 6 N R7 R2 o R R —N\ \R7 R2 o R7 (IV—c) (V—c) (VI-C) or salt thereof. In certain ments, at least one ce of R2 is optionally substituted alkyl, optionally substituted alkenyl, or ally substituted alkynyl. In certain ments, at least one instance of R2 is a group of formula (i). In certain embodiments, at least one instance of R2 is a group of formula (ii). In certain embodiments, at least one instance of R2 is a group of formula (iii). In certain embodiments, L is an optionally substituted alkylene. In certain ments, R6 is a group of formula (i). In certain ments, R6 is a group of formula (ii). In certain embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of formula (i). In certain embodiments, R7 is a group of formula (ii). In certain embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

In certain embodiments of Formulae (IV—a), (V—a), and (VI—a), wherein at least one instance of R2 is a group of formula (i) and each instance of R’ is en, provided is a compound of Formulae (IV—d), (V—d), and (VI—d): @on.32: O R1 RF’Y\_|_/N RPY\_|_/N RPY—/ R(IV—d) R(V-d) (VI-d) or salt thereof. In certain embodiments, at least one ce of R1 is a group of formula (iv).

In certain ments, each instance of R1 is a group of formula (iv). In certain embodiments, R2 is optionally substituted alkyl, optionally substituted alkenyl, or optionally substituted alkynyl. In certain embodiments, R2 is a group of formula (i). In certain embodiments, R2 is a group of formula (ii). In certain embodiments, R2 is a group of formula (iii).

WO 63468 ] In certain embodiments of Formulae (IV—a), (V—a), and (VI—a), n both instances of R2 is a group of formula (i) and each instance of R’ is hydrogen, provided is a compound of Formulae (IV—e), (V—e), and (VI—e): (IV—e) (V—e) (VI—e) or salt thereof. In certain embodiments, at least one instance of R1 is a group of formula (iv).

In certain ments, each ce of R1 is a group of formula (iv).

In certain embodiments of ae (IV—a), (V—a), and (VI—a), wherein at least one instance of R2 is a group of formula (ii) and each ce of R’ is hydrogen, provided is a compound of Formulae (I\72—f), (V—f), and (VI—f): «12:0):?“REMthM O(IV-f) (V-f) (VI-f) or salt thereof. In certain embodiments, at least one instance of R1 is a group of formula (iv).

In certain embodiments, each instance of R1 is a group of formula (iv). In certain embodiments, R2 is optionally substituted alkyl, optionally substituted alkenyl, or optionally substituted alkynyl. In certain embodiments, R2 is a group of formula (i). In certain embodiments, R2 is a group of formula (ii). In certain embodiments, R2 is a group of formula (iii).

In certain embodiments of Formulae (IV—a), (V—a), and (VI—a), wherein both instances of R2 is a group of formula (ii) and each instance of R’ is hydrogen, provided is a compound of Formulae , (V-g), and (VI-g): RLX O O RLX—<O—_\ RLX R1 O WQO N N N 1 R1 R —<N RLX N/ R1 RLx-<—J o H O o o R1 R X‘<—JL (IV-g) (V-g) (VI-g) or salt f. In n ments, at least one instance of R1 is a group of formula (iv).

In certain embodiments, each instance of R1 is a group of formula (iv).

In certain embodiments of Formulae (IV—a), (V—a), and (VI—a), wherein at least one instance of R2 is a group of formula (iii), ed is a compound of Formulae (IV—h), (V—h), and (VI—h): R1 /R2 2 R2\ 0 R\N o R12—N N 0 R1-<N R1 N R1 N Rf FRL-—-’/ C) FzL-J/ (D C) le (IV-h) (V—h) (VI—h) or salt thereof. In certain embodiments, at least one instance of R1 is a group of formula (iv).

In certain embodiments, each instance of R1 is a group of formula (iv). In certain embodiments, R2 is optionally substituted alkyl, optionally substituted alkenyl, or optionally substituted alkynyl. In certain embodiments, R2 is a group of formula (i). In n embodiments, R2 is a group of formula (ii). In certain embodiments, R2 is a group of formula (iii).

In certain embodiments of Formulae (IV—a), (V—a), and (VI—a), wherein both instances of R2 are a group of a (iii), provided is a nd of Formulae (IV—e), (V— e), and (VI—e): RN>L L R1 RL_\N O <: o WQO R1—<N R1 /—N/ R1 N RLJ RL RL-/ 0 o 0 R1 (IV—i) (V—i) (VI—i) or salt thereof. In certain embodiments, at least one instance of R1 is a group of formula (iv).

In certain embodiments, each instance of R1 is a group of formula (iv).

Groups offormula (1'), (ii), and (iii) As understood from the above discussion, APPLs, and in particular, APPL compounds of Formulae (I), (III), (IV), (V), and (VI), each include at least one instance of a group of the formula (i), (ii), or (iii): . R‘ XRL RQ—YRP g—<R- § 0 R'- R' or §_/ (1) (ii) (iii) wherein: each instance of R’ is ndently hydrogen or optionally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, n RY is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted yclyl, optionally substituted heterocyclyl, ally tuted aryl, optionally tuted heteroaryl, or a nitrogen protecting group; RP is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted aryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally substituted heteroC2_50 alkenyl, optionally tuted heteroC2_50 alkynyl, or a polymer.

In the case of Formula (II), the at least one instance of group of formula (i) is incorporated as part of the scaffold, e.g., by monoaddition of a compound (i—X), followed by internal cyclization. See, e.g., Scheme 2.

In certain embodiments, an APPL, and in particular, a compound of Formulae (I), (II), (III), (IV), (V), or (VI), comprises at least one instance of a group of the formula (i) attached thereto: R' (1).

] In certain embodiments of formula (i), Y is O. In certain embodiments of formula (i), Y is S. In certain embodiments of formula (i), Y is NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted aryl, or a nitrogen ting group. In certain embodiments of a (i), Y is NRY, n RY is hydrogen, optionally substituted alkyl, or a nitrogen protecting group. In certain embodiments of formula (i), each instance of R’ is hydrogen.

As used herein, when the group RL is depicted as bisecting a carbon—carbon bond, 6.57., of the group of the formula (i), it is understood that RL may be tuted at either carbon. Nucleophilic attack of an amino or amide group at the least sterically hindered carbon of the epoxide, thiirane, or aziridine of formula (i—X) provides a group of the formula (i—al), (i—a2), or (i—a3) (route a), while nucleophilic attack at the more sterically hindered carbon of the epoxide, thiirane, or ine of formula (i—X) provides a group of the formula , (i—b2), or (i—b3) (route b), wherein RP is hydrogen (Scheme 6). It is understood that compounds of the present invention may comprise a mixture of products attached thereto arising from route (a) and route (b) depending on the preference, or lack thereof, of the mode of addition. The bisecting group RL ed in the Formulae seeks to encompasses all contemplated modes of addition.

Scheme 6.

RP RP RP . R. RL RL R'- RWRL . RP (a) g—N_§ é—NH ("’0 é—NVR/LR' (I-a1) (i-a2) (i-a3) RL g—N—gI or g—NHZ RP RP RP Y RL , R. . RL R' RL R. (b) R\A< —>R R R. R' RL g—N—§ g—NH E—N (i'x) (i-b1) (i-b2) (i-b3) RL The resulting hydroxyl, thiol, or amino group —YRP, wherein RP is hydrogen, may ally be converted to a substituted group, wherein RP is a group other than en, i.e., wherein RP is independently selected from optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally tuted heterocyclyl, optionally substituted aryl, optionally substituted aryl, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a nitrogen protecting group when attached to a en atom; using conventional methods. Alkylation, acylation, and/or protection of a hydroxyl, thiol, or amino moiety are methods well—known in the art; see, e.g., Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, edition, John Wiley & Sons, 1999; Smith and March, March’s Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern s of Organic Synthesis, 3rd Edition, Cambridge sity Press, Cambridge, 1987.

For example, in certain non—limiting embodiments, the yl, thiol, or amino moiety — YRP, wherein RP is hydrogen, may be reacted with an electrophile of the formula RP—X2 wherein RP is a group other than hydrogen, and X2 is a leaving group, to provide a substituted hydroxyl, thiol, and amino group in formula (i).

In certain embodiments of formula (i), RP is hydrogen. In certain embodiments of a (i), RP is optionally substituted alkyl. In certain embodiments of formula (i), RP is optionally substituted alkenyl. In certain embodiments of formula (i), RP is optionally tuted alkynyl. In certain embodiments of formula (i), RP is optionally substituted carbocyclyl. In certain embodiments of formula (i), RP is optionally substituted heterocyclyl.

In certain embodiments of formula (i), RP is optionally substituted aryl. In n embodiments of formula (i), RP is optionally substituted heteroaryl. In certain embodiments of formula (i), RP is an oxygen protecting group when attached to an oxygen atom. In n embodiments of formula (i), RP is a sulfur protecting group when ed to a sulfur atom.

In certain embodiments of formula (i), RP is a nitrogen protecting group when attached to a en atom.

It is understood from the present disclosure that the group of formula (i) represents a group of formula (i—a) or a group of formula (i—b): R' R'- (i—a) (i—b).

In certain embodiments, the reaction mixture es a mixture of APPLs comprising more APPLs conjugated to a group of formula (i—a) than formula (i—b), e.g., the reaction mixture comprises r than 50%, greater than 60%, greater than 70%, greater than 80%, greater than 90%, greater than 95%, greater than 99%, between about 60% to about 100%, between about 70% to about 100%, between about 80% to about 100%, between about 90% to about 100%, between about 95% to about 100%, or between about 99% to about 100%, of an APPL attached to formula (i—a).

In certain embodiments, the epoxide, thiirane, or aziridine of formula (i—x) is chiral, i.e., having (R) or (S) stereochemistry. Chiral es, thiiranes, and aziridines can be obtained from a y of sources which are familiar to those skilled in the art of organic synthesis. In some embodiments, the chiral epoxide, thiirane, or aziridine is obtained cially. In some embodiments, the chiral epoxide, thiirane, or aziridine is synthesized according to methods known to those of skill in the art, such as, but not d to the Sharpless epoxidation of y and secondary allylic alcohols into 2,3—epoxyalcohols (see, e.g., Katsuki et al., J. Am. Chem. Soc. 1980, 102, 5974; Hill et al., Org. Syn, Coll. Vol. 7, p.461 (1990); Vol. 63, p.66 (1985); i et al., Org. React. 1996, 48, 1—300). In some embodiments, the chiral epoxide, thiirane, or aziridine is obtained from the resolution of a mixture (e.g., c mixture) of epoxides, thiiranes, or aziridines. In some embodiments, the chiral epoxide, thiirane, or aziridine is obtained by the separation of enantiomers or diastereoisomers using chiral chromatography. Chirality can be characterized in a variety of ways, e.g., obtaining a crystal structure of the compound containing a heavy atom attached thereto, obtaining the optical rotation of the compound, and/or NMR analysis after al modification of the optically active compound with a chiral derivatizing agent are some methods useful in evaluating ity.

RA”RL R'ARL (1x1) (1x2) RL \' Ra R' R' R' ngRP §~<LYRP 7>~YRP gimp R' R' ER' ERL R's. RL (i—a1) (i—a2) (i—bl) (i—b2) In certain embodiments, wherein the e, thiirane, or aziridine of formula (i—x1) is chiral, the conjugation reaction is elective, and the reaction provides a chiral mixture of APPLs sing more APPLs conjugated to a group of formula (i—a1) than formula (i—b1), 6.57., the reaction mixture ses greater than 50%, greater than 60%, greater than 70%, greater than 80%, greater than 90%, greater than 95%, greater than 99%, between about 60% to about 100%, between about 70% to about 100%, between about 80% to about 100%, between about 90% to about 100%, between about 95% to about 100%, or between about 99% to about 100%, of an APPL attached to formula (i—a1).

In other embodiments, wherein the epoxide, thiirane, or aziridine of formula (i— x2) is chiral, the conjugation reaction is regioselective, and the reaction provides a chiral mixture of APPLs comprising more APPLs conjugated to a group of a (i—a2) than a (i—b2), 6.57., the reaction e comprises greater than 50%, greater than 60%, greater than 70%, r than 80%, greater than 90%, greater than 95%, greater than 99%, between about 60% to about 100%, between about 70% to about 100%, between about 80% to about 100%, n about 90% to about 100%, between about 95% to about 100%, or between about 99% to about 100%, of an APPL attached to a (i—a2).

] In certain embodiments, an APPL, and in particular, a compound of Formulae (I), (II), (III), (IV), (V), or (VI), comprises at least one instance of a group of the formula (ii) attached thereto: R' (ii).

In n embodiments of formula (ii), X is O. In certain embodiments of formula (ii), X is S. In certain embodiments of formula (ii), X is NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group. In certain embodiments of a (ii), X is NRX, wherein RX is hydrogen, optionally substituted alkyl, or a nitrogen protecting group. In certain embodiments of formula (i), each instance of R’ is hydrogen.

In certain embodiments, an APPL, and in particular, a compound of Formulae (I), (II), (III), (IV), (V), or (VI), comprises at least one instance of a group of the formula (ii) attached thereto: (iii).

As generally d above, RL is optionally substituted C150 alkyl, ally substituted C250 alkenyl, optionally substituted C250 l, optionally tuted C150 heteroalkyl, optionally substituted C250 heteroalkenyl, ally tuted C250 heteroalkynyl, or a polymer. The group RL seeks to encompass lipophilic, hydrophobic, and/or non—polar groups, but such terms should not limit the scope of RL.

In certain embodiments, at least one instance of RL is an optionally substituted C150 alkyl. In certain embodiments, RL is an optionally substituted C6_50alkyl. In certain ments, RL is an optionally substituted C6_40alkyl. In certain embodiments, RL is an optionally substituted C6_30alkyl. In n embodiments, RL is an optionally substituted C6- goalkyl. In certain embodiments, RL is an ally substituted Cg_20alkyl. In certain embodiments, RL is an optionally substituted Cgalkyl. In certain embodiments, RL is an optionally tuted Cgalkyl. In certain embodiments, RL is an optionally substituted Cloalkyl. In certain embodiments, RL is an optionally substituted C11alkyl. In certain embodiments, RL is an optionally substituted Clgalkyl. In certain ments, RL is an optionally substituted C13alkyl. In certain embodiments, RL is an optionally substituted C14alkyl. In certain embodiments, RL is an optionally substituted C15alkyl. In n embodiments, RL is an optionally substituted C16alkyl. In certain embodiments, RL is an optionally substituted C17alkyl. In certain embodiments, RL is an optionally substituted Clgalkyl. In certain embodiments, RL is an optionally substituted C19alkyl. In n embodiments, RL is an optionally substituted Czoalkyl. In any of the above embodiments, the group RL is an unsubstituted alkyl group.

In certain embodiments, at least one instance of RL is an unsubstituted alkyl.

Exemplary unsubstituted alkyl groups include, but are not limited to, —CH3, —C2H5, —C3H7, — C4H9, -C5H11,-C6H13, , -C8H17, -C9H19, -C10H21, -C11H23, -C12H25,-C13H27, -C14H29, - , -C16H33, -C17H35, -C18H37, -C19H39, -C20H41, -C21H43, -C22H45, -C23H47, -C24H49, and -C25H51- In certain embodiments, at least one instance of RL is a substituted alkyl. For example, in certain embodimenets, at least one instance of RL is an alkyl substituted with one or more fluorine substituents. Exemplary fluorinated alkyl groups e, but are not limited «9‘ F FFFFFFFFFF FFFF FFFF MW FFFFFFFFF FF FFF F a“ FFFFFFFFFFFF FFFF F tr” FM F FFFFFFF FF FFF ,rr’ F FFFFFF FFFFFFFFFFFFFF FFFFFF PW 9898986;rr F F FFFFFFFFFFFF FF F FFFFFF F FFFFF FFFFFF Fr" F FFFFFFFFFFFFFFF FFFFFFFF FFFFFFFFFFFFFFFF F FFFFF WF s" F FFFFFFFFFFFFFFFF FFFFFFFFFrrrr FFFFFFFFFFFFFFFFF FFFFFFFF x F FFFFFFFFFFFFFFFF FFFF FFFFFFFFFFFF FFFFFFFFF F 9“ FWe! FFFFFFFFFFFFFFFFFF FFFFFFFFFF FFFF FFFFFFFFFFFFFF FFFFFFFFFF WWW FWEFFFFFFFFFFFFFFFFFFF FFFFFFFFFFF In certain embodiments, at least one instance of RL is an optionally substituted C250 alkenyl. In certain embodiments, RL is an optionally substituted C6_50alkenyl. In certain embodiments, RL is an optionally substituted C6_40alkenyl. In certain embodiments, RL is an optionally tuted C6_30alkenyl. In certain ments, RL is an optionally substituted C6_20alkenyl. In n embodiments, RL is an optionally substituted lkenyl.

In certain embodiments, RL is an optionally substituted Cgalkenyl. In n embodiments, RL is an optionally substituted Cgalkenyl. In certain embodiments, RL is an optionally substituted Cloalkenyl. In certain embodiments, RL is an optionally substituted C11alkenyl.

In certain embodiments, RL is an optionally substituted Clzalkenyl. In certain embodiments, RL is an optionally substituted C13alkenyl. In certain embodiments, RL is an optionally substituted C14alkenyl. In certain embodiments, RL is an optionally substituted C15alkenyl.

In certain embodiments, RL is an optionally substituted C16alkenyl. In certain embodiments, RL is an optionally substituted C17alkenyl. In certain embodiments, RL is an optionally tuted Clgalkenyl. In certain ments, RL is an optionally substituted Clgalkenyl.

In certain embodiments, RL is an optionally tuted enyl. In any of the above embodiments, the group RL is an unsubstituted alkenyl group.

Exemplary unsubstituted alkenyl groups include, but are not limited to: /\”H W My“, N63: Wt“: /\/\/\/\/\/\/\/\r‘yv W\/\/\/\/\/\/\\ arr W\ Jr, g Myristoleic —(CH2)7CH=CH(CH2)3CH3, Palmitoliec —(CH2)7CH=CH(CH2)5CH3, Sapienic —(CH2)4CH=CH(CH2)3CH3, Oleic 7CH=CH(CH2)7CH3, Linoleic —(CH2)7CH=CHCH2CH=CH(CH2)4CH3, OL-Linolenic -(CH2)7CH=CHCHZCH=CHCH2CH=CHCH2CH3, Arachinodonic -(CH2)3CH=CHCHZCHzCHCHZCHzCHCHZCHzCH(CH2)4CH3, Eicosapentaenoic —(CH2)3CH=CHCHZCHzCHCHZCH=CHCHZCH=CHCH2CH=CHCH2CH3, Erucic —(CH2)11CH=CH(CH2)7CH3, and Docosahexaenoi — c (CH2)2CH=CHCH2CH=CHCHZCHzCHCHzCHzCHCHZCHzCHCHZCH=C H-CH2CH3.

In embodiments, wherein RL is defined as a C6_50alkyl or C6_50alkenyl , such groups are meant to encompass lipophilic groups (also referred to as a “lipid tail”).

Lipophilic groups comprise a group of molecules that include fats, waxes, oils, fatty acids, and the like. Lipid tails present in these lipid groups can be ted and unsaturated, depending on whether or not the lipid tail comprises double bonds. The lipid tail can also se different lengths, often categorized as medium (i.e., with tails between 7—12 carbons, e.g., C742 alkyl or C742 alkenyl), long (i.e., with tails r than 12 carbons and up 2012/062222 to 22 carbons, e.g., C1342 alkyl or C1342 alkenyl), or very long (i.e., with tails r than 22 carbons, e.g., C2330 alkyl or C2330 alkenyl).

In certain embodiments, RL is an optionally substituted C250 alkynyl. In certain embodiments, RL is an optionally substituted C6_50alkynyl. In certain embodiments, RL is an optionally substituted C640alkynyl. In n embodiments, RL is an optionally substituted lkynyl. In certain embodiments, RL is an optionally substituted C6_20alkynyl. In certain ments, RL is an optionally substituted Cg_20all<ynyl. In certain embodiments, RL is an optionally tuted Cgalkynyl. In certain ments, RL is an ally substituted Cgalkynyl. In certain embodiments, RL is an optionally substituted Cloalkynyl. In certain embodiments, RL is an optionally tuted C11alkynyl. In n embodiments, RL is an optionally substituted Clzalkynyl. In certain embodiments, RL is an optionally substituted C13alkynyl. In certain embodiments, RL is an optionally substituted C14alkynyl. In certain embodiments, RL is an optionally substituted C15alkynyl. In certain embodiments, RL is an optionally substituted C16alkynyl. In certain embodiments, RL is an optionally substituted C17alkynyl. In certain embodiments, RL is an optionally tuted Clgalkynyl. In certain embodiments, RL is an optionally substituted Clgalkynyl. In certain embodiments, RL is an optionally tuted Czoalkynyl. In any of the above ments, the group RL is an unsubstituted l group.

In certain embodiments, at least one instance of RL is an optionally substituted heteroC1_50 alkyl. In certain embodiments, RL is an optionally substituted heteroC6_50 alkyl.

In certain embodiments, RL is an ally substituted heteroC6_40 alkyl. In certain embodiments, RL is an optionally substituted heteroC6_30alkyl. In certain embodiments, RL is an optionally substituted heteroC6_20alkyl. In certain embodiments, RL is an optionally substituted heteroC10_20alkyl. In certain embodiments, RL is an optionally substituted heterngalkyl. In certain embodiments, RL is an optionally substituted heterngalkyl. In certain embodiments, RL is an optionally substituted heteroCloalkyl. In certain ments, RL is an optionally substituted C11alkyl. In n embodiments, RL is an optionally substituted heteroClzalkyl. In certain embodiments, RL is an optionally substituted heteroC13alkyl. In certain embodiments, RL is an optionally substituted heteroC14alkyl. In certain ments, RL is an optionally substituted heteroC15alkyl. In certain embodiments, RL is an optionally substituted heteroC16alkyl. In certain embodiments, RL is an optionally substituted heteroC17alkyl. In certain embodiments, RL is an optionally substituted heteroClgalkyl. In certain embodiments, RL is an optionally substituted heteroClgalkyl. In certain embodiments, RL is an optionally substituted heteroCzoalkyl. In any of the above embodiments, the group RL is an unsubstituted alkyl group.

Exemplary unsubstituted heteroalkyl groups include, but are not limited to, \O/\..r"r W\/\/\O/\rr,.r /\o/\ve‘ /\/\/\/\/\O/\rfi.r V\O/\(H’ W\/\/\/\O/\;,: /\/\O/\rrrr /\/\/\/\/\/\O/\‘J,J \/\/\/\/\/\/\O/\ WOAé-‘I NWOj‘44: : WOAHH /\/\/\/\/\ /\O V\/\/\O/\IJJJ r51 In certain embodiments, at least one instance of RL is an optionally substituted heteroC2_50alkenyl. In certain embodiments, RL is an ally substituted heteroC6_ 50alkenyl. In certain embodiments, RL is an optionally substituted heteroC6_40alkenyl. In certain embodiments, RL is an optionally tuted heteroC6_30alkenyl. In certain embodiments, RL is an optionally substituted heteroC6_20alkenyl. In certain embodiments, RL is an optionally substituted heterng_20alkenyl. In certain embodiments, RL is an optionally substituted heterngalkenyl. In certain embodiments, RL is an optionally substituted heterngalkenyl. In certain embodiments, RL is an optionally substituted heteroCloalkenyl.

In certain embodiments, RL is an optionally substituted heteroC11alkenyl. In certain embodiments, RL is an optionally tuted Clzalkenyl. In certain ments, RL is an optionally substituted heteroC13alkenyl. In n embodiments, RL is an optionally substituted heteroC14alkenyl. In certain embodiments, RL is an optionally substituted heteroC15alkenyl. In certain embodiments, RL is an optionally substituted heteroC16alkenyl.

In certain embodiments, RL is an ally substituted heteroC17alkenyl. In certain embodiments, RL is an ally substituted heteroClgalkenyl. In certain embodiments, RL is an ally substituted heteroC19alkenyl. In certain embodiments, RL is an ally substituted heteroCzoalkenyl. In any of the above embodiments, the group RL is an unsubstituted heteroalkenyl group.

In certain embodiments, RL is an optionally substituted heteroC2_50alkynyl. In certain embodiments, RL is an optionally substituted heteroC6_50alkynyl. In certain embodiments, RL is an optionally tuted heteroC6_40alkynyl. In certain embodiments, RL is an optionally substituted heteroC6_30alkynyl. In certain embodiments, RL is an optionally substituted heteroC6_20alkynyl. In certain embodiments, RL is an optionally substituted g_20alkynyl. In certain embodiments, RL is an optionally substituted heterngalkynyl.

In certain embodiments, RL is an optionally substituted heterngalkynyl. In certain embodiments, RL is an optionally substituted heteroCloalkynyl. In n embodiments, RL is an optionally substituted heteroC11alkynyl. In certain embodiments, RL is an optionally substituted heteroClgalkynyl. In certain embodiments, RL is an optionally substituted heteroC13alkynyl. In certain embodiments, RL is an ally substituted heteroC14alkynyl.

In n embodiments, RL is an optionally substituted heteroC15alkynyl. In certain embodiments, RL is an optionally substituted C16alkynyl. In n embodiments, RL is an optionally substituted heteroC17alkynyl. In n embodiments, RL is an optionally substituted heteroClgalkynyl. In certain embodiments, RL is an optionally substituted heteroClgalkynyl. In certain embodiments, RL is an optionally substituted Czoalkynyl.

In any of the above embodiments, the group RL is an unsubstituted heteroalkynyl group.

In certain embodiments, at least one instance of RL is a polymer. As used herein, a “polymer” refers to a compound comprised of at least 3 (e.g., at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, etc.) repeating covalently bound structural units. The polymer is in certain embodiments patible (i. 6., non—toxic). ary polymers include, but are not limited to, cellulose polymers (e.g., hydroxyethylcellulose, ethylcellulose, carboxymethylcellulose, methylc cellulose, ypropylmethylcellulose (HPMC)), dextran polymers, leic acid polymers, poly(acrylic acid) polymers, poly(vinylalcohol) polymers, polyvinylpyrrolidone (PVP) polymers, and polyethyleneglycol (PEG) polymers, and combinations thereof.

Additional Methods ofPreparation As described herein, in order to provide compounds of the t invention, an APPL precursor is treated with one or more conjugating reagents, e.g., selected from an epoxide, thiirane, or aziridine of formula (i—X), an OL,B—unsaturated ester, thioester, or amide of formula (ii—X), or an an aldehyde of formula (iii—X), to provide the APPL.

R' o O . R' R\A<RL RIJYkXRL HJLRL (i-x) (ii-x) (iii-x) ] For example, in one aspect, provided is a method of preparing an APPL functionalized with a group of formula (i) comprising heating the precursor in an organic solvent (e.g., EtOH) with one or more conjugating reagents of formula (i—x) to provide the desired APPL. In certain embodiments, the mixture is heated n about 100 to about 200 OC, inclusive, e.g., about 150 0C.

In another aspect, provided is a method of preparing an APPL functionalized with a group of formula (ii) comprising heating the precursor in an organic solvent (e.g., EtOH) with one or more conjugating reagents of formula (ii—x) to provide the desired APPL.

In certain embodiments, the mixture is heated between about 50 to about 100 OC, ive, e.g., about 90°C.

In another aspect, provided is a method of preparing an APPL functionalized with a group of formula (iii) comprising mixing the precursor in an organic solvent (e.g., THF) with one or more conjugating reagents of formula (iii—x) and a reducing agent (e.g., NaBH(OAc)3) to provide the desired APPL. In certain embodiments, the temperature of the on mixture is room temperature mixture.

In certain embodiments, n only one conjugating reagent is used, each instance of RL is the same in the APPL. For example, in certain embodiments, each instance of RL is the same wherein RL is an optionally substituted alkyl. In certain embodiments, each instance of RL is the same wherein RL is an unsubstituted alkyl. In n embodiments, each instance of RL is the same wherein RL is selected from the group consisting of —CH3, — C2H5, -C3H7, -C4H9, -C5H11, -C6H13, -C7H15, -C8H17, -C9H19, -C10H21, -C11H23, -C12H25, - C13H27, -C14H29, -C15H31, -C16H33, -C17H35, 7, -C19H39, and -C20H41- In n embodiments, each instance of RL is the same wherein RL is an l group selected from — CsH17, -C9H19, -C10H21, -C11H23, 5,-C13H27, 9, -C15H31, and 3- Alternatively, in certain embodiments, wherein more than one conjugating reagent is used in the conjugation reaction (e.g., two, three, four, five, six, seven, eight, nine, or ten different conjugating ts), the APPL may comprise two or more (e.g. , two, three, four, five, six, seven, eight, nine, or ten) different groups of the formula (i), (ii), and/or (iii) attached thereto.

For example, in certain embodiments, two different epoxides are used in the conjugation on. In this instance, in certain embodiments, the APPL comprises two different RL groups. For example, in certain embodiments, the APPL comprises a mixture of two ent RL groups, wherein the first RL group is an optionally substituted alkyl, and the second RL group is a polymer.

As would be appreciated by one of skill in this art, the degree of conjugation may be controlled by the reaction conditions (e.g. , temperature, starting materials, concentration, solvent, etc.) used in the synthesis. The synthesized APPL may be purified by any technique known in the art including, but not limited to, precipitation, crystallization, chromatography, distillation, etc.

In certain embodiments, the APPL is isolated as a salt. For example, in certain embodiments, the APPL is d with an acid (e. 57., an c acid or inorganic acid) to form the ponding salt. In other embodiments, tertiary amines are ted to form a quaternary ammonium salt of the APPL. The tertiary amines may be alkylated with any alkylating agent, for example, alkyl s such as methyl iodide may be used to from the quaternary amino groups. The anion associated with the quaternary amine may be any organic or inorganic anion. In certain embodiments, the anion is a pharmaceutically acceptable anion.

The invention also provides libraries of APPLs ed by the inventive methods. For example, in certain embodiments, provided is a method of ing a compound library, the method comprising providing a plurality of different APPLs, or salts thereof; and performing at least one assay with the compound library to determine the presense or e of a desired ty. These APPLs may be ed and/or screened using high—throughput techniques involving liquid handlers, robots, microtiter plates, computers, etc. In certain ments, the APPLs are screened for their ability to transfect polynucleotides or other agents (e. 57., proteins, es, small molecules) into the cell. For example, in one embodiment, ed is a method of screening a compound library, the method comprising providing a plurality of two or more different APPLs and screening the compound library for a desired property.

In one embodiment, a library of different APPLs is prepared in parallel. A different precursor and/or conjugating reagent is added to each vial in a set of vials or to each well of a multi—well plate used to prepare the library. The array of reaction es is incubated at a temperature and length of time sufficient to allow formation of the APPL. The APPL may then be isolated and purified using techniques known in the art. The APPL may then be screened using high—throughput techniques to identify APPLs with a desired property, e. g. wherein the desired property is solubility in water, solubility at different pH, ability to bind polynucleotides, ability to bind heparin, ability to bind small molecules, ability to bind protein, y to form microparticles, ability to increase tranfection efficiency, ability to support cell growth, y to support cell attachment, ability to support tissue growth, and/or intracellular ry of the APPL and/or an agent complexed or attached thereto to aid in bioprocessing, e. g., for the purpose of manufacturing proteins. In certain embodiments the APPLs may be screened for properties or teristics useful as coatings, additives, materials, and excipients in biotechnology and biomedical applications such as the coating of medical devices or implants with films or ayer films, as non—biofouling agents, micropatterning agents, and cellular ulation agents. In n embodiments the APPL may be screened for properties or characteristics useful in gene therapy (e.g. , the y to bind polynucleotides and/or increase in transfection efficiency), bioprocessing (e.g., aiding in the intracellular manufacturing of proteins), or the administration and/or delivery of a therapeutic agent (e.g., cleotide, small molecule, antigen, drug, protein, peptide, etc.) to a subject, tissue, organ, or cell.

Exemplary Compounds ofthe Present Invention Certain compounds of the present invention are specifically contemplated herein. For e, compounds comprising unsubstituted n—alkyl RL groups containing 8, 9, , ll, 12, 13, and 14 carbon atoms are specifically contemplated. In certain embodiments R1 of such nds is an amino acid side chain as defined in Table l of the Examples.

Exemplary amino acid, peptide, and polypeptide compounds of Formula (I) include, but are not limited to: H0C8H17R 9R ORA4 ORA4 HO \C8H17 HO \C9H19 9 9 1 1 HOC10H21 R HO\—C11H23 R ORA4 ORA4 HO \C10H21 HO \OC11H23 9 9 HOC12H25 R1 HO\C13H27 R1 ORA4 ORA4 HO \OC12H25 HOf\OC13H27 9 9 HO\—C14H29R ORA4 HOf\OC14Hzg O O 1 1 N N N ORA4 N ORA4 O n R1 O n R1 CsH17—O O o O , , O O C10H21—O/<fi R 1 O R 1 O H H N C11"‘23—O%fl N N 0RA4 N 0RA4 O n R1 O n R1 C10Hz1—O C11H23—O o o O O C12H25—0/</\ R1 O R 1 O H C13H27—0//</\ H N N N ORA4 N ORA4 O n R1 O n R1 C12st—O C13Hz7—O o o C14H29—O//</\ R1 O N ORA4 o n R1 (314st;—0 o o C8H17—”/<fi R 1 O 1 R O H C9H19—”/<fi H N N N ORA4 N ORA4 O n R1 O n R1 C H —Ns 17 C H —N9 19 H O H O O O (WWW—Mk R 1 O 1 O H Cums—”k R H N N N 0RA4 N 0RA4 O n R1 O n R1 C10H —N21 C11 H —N23 H O H O O O C12H25—”/</\ R1 O 1 R O H C13H27—HJ</\ H N N N ORA4 N ORA4 o n R1 o n R1 C12H —N25 C 13H —N27 H O H O N 0RA4 o n R1 C14H —N29 H O \JN»F1\n/NNMORA4CaH17J C9H19/\JN»F1\H/N“IMORA409H19J C10H21/\JN,P1\n/NNMORA“ C11"|2s/\JNAPYNNMORA“C10H21J C11H23J R1 o R1 o H H C12Hz5/\ N C13Hz7/\ N N ORA4 N ORA4 C12H25J n R 1 C13H27J n R 1 O O , , R1 o 9/\ N N 0RA4 C14l‘l29 O n R1 and salts thereof.

Exemplary cyclized compounds of Formula (11), include, but are not limited to: O O O O R1 R1 R1 R1 O O O O HN\)\ HN\)\ HN\)\ HN\)\ CsH17, C9H19, C10H21 (311st o o 0 R1 R1 R1 O O 0 0 HN\)\ HN\)\ HN\)\ HOA/VwkCsH17 , C13H27, C14H29 CSH17 , , O O O R1 R1 R1 O O O HO/\/\/N\J\ HO/\/\/N\)\ N ch19 C10H21 HO/\/\/ C11H23 CQH19 C10Hz1 C11H23 , , , O O O R1 R1 R1 O O 0 HO/\/\/wk wk N C12H25 HO/\/\/ C13H27 HO/\/\/ C14H29 C12Hz5 C13Hz7 and C14"‘29 , , , and salts thereof.

Exemplary cyclic dipeptide and cyclic ptide compounds of Formula (111) include, but are not limited to: 2012/062222 HO C1on1 \|—\ O O HO C12H25 |—\ x|_\ N N HO C14"‘29 \l_\ WO 63468 2012/062222 and, in particular, cyclic—KK and polycyclic lysine APPLs of the formula: CsH17\ WO 63468 2012/062222 CgH1g—O C12"‘25“O C14H29_O CBH17_NH CsH17 H O CgH19‘NH CQH’IQ 2012/062222 C10H21_NH C11H23‘NH O O HN\ HN\ C10H21 C11H23 H O H O C H —N C12H25—N 13 27 O O C12H25‘NH C13H27—NH C10H21 C10H21 /_ /_ C13H27 > C14H29 > C13Hz7 and C14H29 and salts f.

Compositions The present invention contemplates an APPL as a component of a composition.

For example, in certain embodiments, provided is a ition comprising an APPL, or salt thereof, and an excipient, wherein the APPL is an amino acid, a linear or cyclic peptide, or a linear or cyclic polypeptide, or structural isomer thereof, and wherein an amino or amide group of the APPL is conjugated to a group of formula (i), (ii), or (iii). In certain embodiments, the group of formula (i), (ii), or (iii) is attached to an amino group present on the APPL ld.

Compositions, as described herein, comprising an APPL and an excipient of some sort may be useful in a variety of medical and dical applications. For example, pharmaceutical compositions comprising an APPL and an ent may be useful in the delivery of an effective amount of an agent to a subject in need thereof. Nutraceutical compositions comprising an APPL and an excipient may be useful in the delivery of an effective amount of a nutraceutical, e.g., a dietary supplement, to a subject in need thereof.

Cosmetic compositions comprising an APPL and an excipient may be ated as a cream, ointment, balm, paste, film, or liquid, etc, and may be useful in the application of make—up, hair ts, and materials useful for personal hygiene, etc. Compositions comprising an APPL and an excipient may be useful for non—medical applications, e.g., such as an on or fier, useful, for example, as a food component, for extinguishing fires, for disinfecting surfaces, for oil cleanup, etc.

Peptides play significant roles in endogenous cellular signaling and trafficking pathways, and offer tremendous potential in leveraging such interactions to enhance the delivery efficiency of systems which incorporate e moieties. Thus, compositions comprising an APPL and an ent may further be useful in bioprocessing, such as a cell’s bioprocessing of a cially useful chemical or fuel. For example, intracellular delivery of the APPL or an agent complexed o may be useful in bioprocessing by maintaining the cell’s health and/or growth, e.g., in the manufacturing of proteins.

The composition may comprise one type of APPL but may also comprise any number of different types of APPLs, e.g., l, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different types of APPLs.

In certain embodiments, the composition further comprises an agent, as described herein. For e, in certain embodiments, the agent is a small molecule, organometallic compound, nucleic acid, protein, peptide, cleotide, metal, targeting agent, an isotopically labeled chemical nd, drug, vaccine, immunological agent, or an agent useful in bioprocessing. In certain embodiments, the agent is a polynucleotide. In certain embodiments, the polynucleotide is DNA or RNA. In certain embodiments, the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA. In certain embodiments, the polynucleotide and the one or more APPLs are not ntly attached.

In certain embodiments, the one or more APPLs are in the form of a particle. In certain embodiments, the particle is a nanoparticle or microparticle. In certain embodiments, the one or more APPLs are in the form of liposomes or micelles. It is understood that, in certain embodiments, these APPLs self—assemble to provide a particle, micelle, or liposome.

In certain embodiments, the particle, micelle, or liposome encapsulates an agent. The agent to be delivered by the particle, micelle, or me may be in the form of a gas, liquid, or solid. The APPLs may be ed with polymers (synthetic or l), surfactants, cholesterol, carbohydrates, proteins, lipids etc. to form the particles. These particles may be further combined with an excipient to form the composition.

“Excipients” include any and all solvents, diluents or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic , thickening or emulsifying , preservatives, solid binders, ants and the like, as suited to the particular dosage form desired. General considerations in formulation and/or manufacture can be found, for e, in Remington ’s Pharmaceutical Sciences, Sixteenth Edition, E.

W. Martin (Mack hing Co., Easton, Pa., 1980), and Remington: The Science and Practice ofPharmacy, 21st Edition (Lippincott Williams & Wilkins, 2005).

Exemplary excipients include, but are not limited to, any non—toxic, inert solid, semi—solid or liquid filler, t, encapsulating material or formulation auxiliary of any type. Some examples of materials which can serve as excipients include, but are not limited to, sugars such as lactose, glucose, and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose, and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; er oil; sesame oil; olive oil; corn oil and soybean oil; glycols such as propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; detergents such as Tween 80; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen—free water; isotonic saline; Ringer’s on; ethyl l; and phosphate buffer solutions, as well as other xic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, g agents, sweetening, flavoring and ing agents, preservatives and antioxidants can also be t in the composition, according to the judgment of the formulator. As would be appreciated by one of skill in this art, the 2012/062222 excipients may be chosen based on what the composition is useful for. For example, with a pharmaceutical composition or cosmetic composition, the choice of the excipient will depend on the route of administration, the agent being delivered, time course of delivery of the agent, etc, and can be administered to humans and/or to animals, orally, rectally, parenterally, intracistemally, intravaginally, intranasally, intraperitoneally, topically (as by powders, creams, ointments, or drops), bucally, or as an oral or nasal spray.

Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline ose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, etc, and combinations thereof. ary granulating and/or dispersing agents include potato , corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose and wood products, natural sponge, cation—exchange resins, calcium carbonate, silicates, sodium carbonate, cross—linked poly(vinyl—pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross—linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, atinized starch (starch 1500), rystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, nary ammonium nds, etc, and combinations thereof.

Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g. bentonite [aluminum silicate] and Veegum [magnesium aluminum silicate]), long chain amino acid derivatives, high molecular weight alcohols (e.g. stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and ene glycol earate, polyvinyl alcohol), ers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid r, and carboxyvinyl r), carrageenan, cellulosic derivatives (e.g. carboxymethylcellulose sodium, ed cellulose, hydroxymethyl ose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g. yethylene sorbitan urate [Tween 20], polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan monooleate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan monostearate [Span 60], an tristearate [Span 65], glyceryl monooleate, sorbitan monooleate [Span 80]), polyoxyethylene esters (e.g. 2012/062222 yethylene monostearate [Myrj 45], polyoxyethylene hydrogenated castor oil, hoxylated castor oil, polyoxymethylene stearate, and Solutol), sucrose fatty acid , hylene glycol fatty acid esters (e.g. Cremophor), polyoxyethylene ethers, (e.g. polyoxyethylene lauryl ether [Brij 30]), poly(vinyl—pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F 68, Poloxamer 188, cetrimonium e, cetylpyridinium chloride, benzalkonium chloride, te sodium, etc. and/or combinations thereof.

Exemplary binding agents include starch (e.g. cornstarch and starch paste), gelatin, sugars (e.g. sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, eta), natural and synthetic gums (e.g. , sodium alginate, t of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, ypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, ose acetate, poly(vinyl—pyrrolidone), magnesium aluminum silicate (Veegum), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, eta, and/or combinations thereof.

Exemplary preservatives include idants, chelating agents, antimicrobial vatives, antifungal preservatives, alcohol preservatives, acidic preservatives, and other vatives.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl e, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.

Exemplary chelating agents e ethylenediaminetetraacetic acid (EDTA) and salts and es thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, honium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal. ary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium te, sodium propionate, and sorbic acid.

] Exemplary alcohol preservatives include ethanol, polyethylene , phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.

] Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta— carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.

Other vatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate , sodium ite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben, Germall llS, Germaben II, Neolone, Kathon, and Euxyl. In n embodiments, the preservative is an anti—oxidant. In other embodiments, the preservative is a chelating agent.

Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, m citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D— ic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, m hydroxide phosphate, ium acetate, ium chloride, potassium ate, potassium es, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium e, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate es, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen—free water, isotonic saline, Ringer’s solution, ethyl alcohol, etc, and combinations thereof.

Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, etc, and combinations thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, a, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening se, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea , macademia nut, mallow, mango seed, foam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils.

Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, icone 360, pyl myristate, l oil, octyldodecanol, oleyl l, silicone oil, and combinations thereof.

Additionally, the composition may comprise a phospholipid. Exemplary phospholipids include, but are not limited to, disteroylphosphatidylcholine (DSPC), dimyristoylphosphatidylcholine , Dipalmitoylphosphatidylcholine (DPPC), and dioleoyl—sn—glycero—3—phosphocholine (DOPC), l,2—Dilauroyl—sn—Glycero—3—Phosphocholine (dilauroylphosphatidylcholine, DLPC), l,2—Dimyristoyl—sn—Glycero—3—Phosphocholine (dimyristoylphosphatidylcholine, DMPC), l,2—Dipentadecanoyl—sn—Glycero—3— Phosphocholine (dipentadecanoylphosphatidylcholine, DPDPC), l,2—dipalmitoyl—sn—Glycero— 3—Phosphocholine (dipalmitoylphosphatidylcholine, DPPC), l—Myristoyl—2—Palmitoyl—sn— Glycero—3—Phosphocholine (l—myristoyl—2—palmitoylphosphatidylcholine, MPPC), 1,2— Dimyristoyl—sn—Glycero—3—[Phospho—rac—(l—glycerol)] (DMPG), and myristoyl—3— Trimethylammonium—propane.

Additionally, the composition may further comprise a polymer. Exemplary polymers contemplated herein include, but are not limited to, cellulosic polymers and copolymers, for example, cellulose ethers such as methylcellulose (MC), hydroxyethylcellulose (HEC), ypropyl cellulose (HPC), hydroxypropyl methyl cellulose (HPMC), methylhydroxyethylcellulose (MHEC), methylhydroxypropylcellulose (MHPC), carboxymethyl cellulose (CMC) and its various salts, including, e.g., the sodium salt, hydroxyethylcarboxymethylcellulose (HECMC) and its various salts, carboxymethylhydroxyethylcellulose (CMHEC) and its various salts, other ccharides and ccharide derivatives such as starch, n, dextran derivatives, chitosan, and alginic acid and its various salts, carageenan, varoius gums, ing xanthan gum, guar gum, gum arabic, gum , gum ghatti, konjac and gum tragacanth, glycosaminoglycans and proteoglycans such as onic acid and its salts, proteins such as gelatin, collagen, albumin, and fibrin, other polymers, for example, polyhydroxyacids such as polylactide, polyglycolide, polyl(lactide—co—glycolide) and poly(.epsilon.—caprolactone—co—glycolide)—, 2012/062222 yvinyl polymers and their salts (e.g., carbomer), polyvinylpyrrolidone (PVP), polyacrylic acid and its salts, polyacrylamide, polyacilic acid/acrylamide copolymer, polyalkylene oxides such as polyethylene oxide, polypropylene oxide, poly(ethylene oxide— propylene , and a Pluronic r, polyoxyethylene (polyethylene glycol), polyanhydrides, polyvinylalchol, polyethyleneamine and rridine, polyethylene glycol (PEG) polymers, such as PEGylated lipids (e.g.,PEG—stearate, l,2—Distearoyl—sn—glycero—3— Phosphoethanolamine—N—[Methoxy(Polyethylene glycol)—1000], l,2—Distearoyl—sn—glycero—3— Phosphoethanolamine—N—[Methoxy(Polyethylene glycol)—2000], and stearoyl—sn— glycero—3—Phosphoethanolamine—N—[Methoxy(Polyethylene glycol)—5000]), copolymers and salts thereof.

] Additionally, the composition may further comprise an emulsifying agent. ary emulsifying agents include, but are not limited to, a polyethylene glycol (PEG), a polypropylene glycol, a polyvinyl alcohol, a poly—N—vinyl pyrrolidone and copolymers thereof, poloxamer nonionic surfactants, neutral water—soluble polysaccharides (e.g., dextran, , celluloses), non—cationic poly(meth)acrylates, tionic polyacrylates, such as poly(meth)acrylic acid, and esters amide and hydroxyalkyl amides thereof, natural emulsifiers (e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, terol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g. bentonite [aluminum silicate] and Veegum [magnesium aluminum silicate]), long chain amino acid derivatives, high molecular weight alcohols (e.g. stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin earate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl r), carrageenan, cellulosic tives (e.g. carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), an fatty acid esters (e.g. polyoxyethylene sorbitan monolaurate [Tween 20], polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan monooleate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan earate [Span 60], sorbitan tristearate [Span 65], glyceryl monooleate, sorbitan monooleate [Span 80]), polyoxyethylene esters (e.g. polyoxyethylene monostearate [Myrj 45], polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g. Cremophor), polyoxyethylene ethers, (e.g. polyoxyethylene lauryl ether [Brij 30]), poly(vinyl—pyrrolidone), diethylene glycol monolaurate, triethanolamine , sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, etc. and/or combinations thereof. In certain embodiments, the emulsifying agent is terol.

Additionally, the composition may further comprise an apolipoprotein. Previous studies have ed that Apolipoprotein E (ApoE) was able to enhance cell uptake and gene silencing for a certain type of als. See, e. g., Akinc, A., et al., Targeted delivery ofRNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol Ther. 18(7): p. 1357—64. In certain embodiments, the apolipoprotein is ApoA, ApoB, ApoC, ApoE, or ApoH, or an isoform thereof.

Liquid compositions e emulsions, microemulsions, ons, suspensions, syrups, and elixirs. In addition to the APPL, the liquid composition may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl e, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3—butylene glycol, dimethylformamide, oils (in particular, cottonseed, nut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and es thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.

Injectable compositions, for example, able aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or g agents and suspending agents. The sterile injectable preparation may also be a able solution, suspension, or emulsion in a nontoxic parenterally acceptable diluent or t, for example, as a solution in 1,3—butanediol. Among the acceptable vehicles and solvents for pharmaceutical or cosmetic compositions that may be employed are water, Ringer’s solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. Any bland fixed oil can be employed including synthetic mono— or diglycerides. In on, fatty acids such as oleic acid are used in the preparation of injectables. In certain embodiments, the particles are suspended in a carrier fluid comprising 1% (w/v) sodium carboxymethyl ose and 0.1% (v/v) Tween 80. The able composition can be ized, for e, by filtration through a bacteria—retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use. ] itions for rectal or vaginal stration may be in the form of suppositories which can be prepared by mixing the particles with suitable non—irritating excipients or carriers such as cocoa butter, polyethylene glycol, or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the particles.

Solid itions include capsules, tablets, pills, powders, and granules. In such solid compositions, the particles are mixed with at least one excipient and/or a) s or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for e, carboxymethylcellulose, alginates, gelatin, nylpyrrolidinone, sucrose, and acacia, c) ants such as glycerol, d) disintegrating agents such as agar—agar, calcium carbonate, potato or a starch, alginic acid, certain silicates, and sodium ate, e) on retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and ol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene s, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets, and pills, the dosage form may also comprise buffering agents. Solid compositions of a r type may also be employed as fillers in soft and hard—filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

Tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.

] Solid compositions of a similar type may also be employed as fillers in soft and hard—filled n capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

Compositions for topical or transdermal administration include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants, or patches. The APPL is admixed with an excipient and any needed preservatives or buffers as may be required.

Ophthalmic formulation, ear drops, and eye drops are also contemplated as being within the scope of this invention.

The ointments, pastes, creams, and gels may n, in addition to the APPL, excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, anth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc, and zinc oxide, or es thereof.

Powders and sprays can contain, in addition to the APPL, excipients such as lactose, talc, c acid, aluminum hydroxide, calcium silicates, and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants such as chlorofluorohydrocarbons.

Transdermal patches have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms can be made by dissolving or dispensing the microparticles or nanoparticles in a proper medium. Absorption ers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the particles in a polymer matrix or gel.

Agents ] Agents to be delivered by the systems described herein may be therapeutic, diagnostic, or prophylactic agents. Any chemical compound to be administered to a subject may be delivered using the xes, picoparticles, nanoparticles, microparticles, micelles, or liposomes, described herein. The agent may be an organic molecule (e.g., a therapeutic agent, a drug), inorganic molecule, nucleic acid, protein, amino acid, peptide, polypeptide, cleotide, targeting agent, isotopically labeled organic or nic molecule, vaccine, immunological agent, etc.

] In certain embodiments, the agents are organic molecules with pharmaceutical activity, 6.57., a drug. In certain embodiments, the drug is an antibiotic, anti—viral agent, anesthetic, steroidal agent, anti—inflammatory agent, anti—neoplastic agent, anti—cancer agent, n, vaccine, antibody, decongestant, antihypertensive, sedative, birth control agent, progestational agent, anti—cholinergic, analgesic, anti—depressant, anti—psychotic, B—adrenergic blocking agent, diuretic, cardiovascular active agent, tive agent, non—steroidal anti— inflammatory agent, nutritional agent, etc.

In certain embodiments of the present invention, the agent to be delivered may be a mixture of agents. stic agents include gases; metals; cially available imaging agents used in positron emissions tomography (PET), computer assisted tomography (CAT), single 2012/062222 photon emission computerized tomography, x—ray, fluoroscopy, and ic resonance imaging (MRI); and contrast . Examples of suitable materials for use as contrast agents in MRI include gadolinium chelates, as well as iron, magnesium, manganese, copper, and chromium. Examples of materials useful for CAT and x—ray imaging include iodine— based materials.

Therapeutic and prophylactic agents include, but are not limited to, antibiotics, ional supplements, and vaccines. Vaccines may comprise isolated proteins or peptides, inactivated organisms and viruses, dead organisms and viruses, genetically altered organisms or s, and cell extracts. Therapeutic and prophylactic agents may be combined with interleukins, interferon, cytokines, and adjuvants such as cholera toxin, alum, Freund’s adjuvant, etc. Prophylactic agents include antigens of such bacterial organisms as Streptococccus pneumoniae, Haemophilus influenzae, Staphylococcus , Streptococcus pyrogenes, Corynebacterium diphtheriae, Listeria monocytogenes, Bacillus anthracis, Clostridium tetani, Clostridium botulinum, Clostridium perfringens, Neisseria meningitidis, Neisseria gonorrhoeae, Streptococcus mutans, Pseudomonas aeruginosa, Salmonella typhi, Haemopliilus parainfluenzae, Bordetella pertussis, Francisella tularensis, Yersinia pestis, Vibrio ae, Legionella phila, Mycobacterium ulosis, Mycobacterium leprae, Treponema um, Leptospirosis ogans, Borrelia burgdorferi, Campliylobacterjejuni, and the like; antigens of such s as smallpox, influenza A and B, respiratory syncytial virus, parainfluenza, measles, HIV, varicella—zoster, herpes simplex l and 2, cytomegalovirus, Epstein—Barr virus, rus, rhinovirus, adenovirus, papillomavirus, poliovirus, mumps, , rubella, coxsackieviruses, equine encephalitis, Japanese encephalitis, yellow fever, Rift Valley fever, tis A, B, C, D, and E virus, and the like; antigens of fungal, protozoan, and parasitic organisms such as Cryptococcus neoformans, Histoplasma capsulatum, Candida ns, Candida tropicalis, Nocardia asteroides, Rickettsia sii, Rickettsia typhi, Mycoplasma pneumoniae, Chlamydial psittaci, dial trachomatis, Plasmodiumfalciparum, Trypanosoma brucei, Entamoeba histolytica, Toxoplasma gondii, Trichomonas vaginalis, Schistosoma mansoni, and the like.

These antigens may be in the form of Whole killed organisms, peptides, proteins, glycoproteins, carbohydrates, or combinations thereof.

Targeting Agents Since it is often desirable to target a particular cell, collection of cells, or tissue, an APPL, and the complexes, liposomes, micelles, microparticles, picoparticles and rticles, prepared therefrom, may be modified to include ing agents or targeting regions. For example, the APPL scaffold may include a targeting region. A variety of agents or regions that target particular cells are known in the art. See, e. g., Cotten et al., Methods Enzym. 217:618, 1993. The targeting agents may be included throughout the particle or may be only on the surface. The targeting agent may be a protein, peptide, carbohydrate, rotein, lipid, small molecule, nucleic acids, etc. The targeting agent may be used to target specific cells or tissues or may be used to promote endocytosis or phagocytosis of the le. Examples of targeting agents include, but are not limited to, antibodies, fragments of antibodies, low—density lipoproteins , transferrin, asialycoproteins, gp120 pe protein of the human immunodeficiency virus (HIV), carbohydrates, receptor ligands, sialic acid, aptamers, etc. If the targeting agent is included throughout the particle, the targeting agent may be included in the mixture that is used to form the particles. If the targeting agent is only on the surface, the targeting agent may be associated with (i.e., by covalent, hydrophobic, hydrogen bonding, van der Waals, or other interactions) the formed particles using standard chemical techniques.

Polynucleotide Complexes The present invention contemplates APPLs are particularly useful in the administration of polynucleotides. For example, APPLs comprise secondary or tertiary amines, and, although these amines are hindered, they are available to non—covalently interact with a cleotide (e. g., DNA, RNA, synthetic analogs of DNA and/or RNA, A hydrids, etc.). Polynucleotides or derivatives thereof are contacted with an APPL under conditions suitable to form a polynucleotide/APPL non—covalent complex. The interaction of the APPL with the polynucleotide is thought to at least partially t the degradation of the polynucleotide. By neutralizing the charge on the backbone of the polynucleotide, the l or ly—positively—charged complex is also able to more easily pass through the hydrophobic nes (e.g., cytoplasmic, lysosomal, endosomal, nuclear) of the cell. In certain embodiments, the x is slightly positively charged. In certain embodiments, the complex has a ve ntial. In certain embodiments the C—potential is between 0 and +30.

In one aspect, provided is a method of delivering a polynucleotide to a biological cell, comprising providing a composition comprising an APPL, or salt thereof, and a polynucleotide; and ng the composition to the biological cell under conditions sufficient to facilitate delivery of the polynucleotide into the or of the ical cell; wherein the APPL is an amino acid, a linear or cyclic peptide, or a linear or cyclic polypeptide, or structural isomer f, wherein an amino or amide group of the APPL is ated to a group of formula (i), (ii), or (iii). In certain embodiments, the method is an in viva method. In certain embodiments, the method is an in vitro method.

] An APPL may be at least partially provided as a salt (e.g., is protonated) so as to form a complex with the negatively charged cleotide. In n embodiments, the polynucleotide/APPL complex form particles that are useful in the delivery of polynucleotides to cells. In certain embodiments, more than one APPL may be associated with a polynucleotide molecule. For example, the complex may include 1—100 APPLs, 1— 1000 APPLs, 10—1000 APPLs, or 100—10,000 APPLs associated with a polynucleotide molecule.

Increasing nitrogen:phosphate ratios have been shown to positively influence delivery of genetic al by increasing nucleic acid binding and negatively influence delivery by increasing toxicity. See, e.g., Incani et al., Soft Matter (2010) 6:2124—2138. In certain embodiments, the nitrogen:phosphate ratio (Le. the ratio between the amino groups present in the APPL, and the phosphate groups t in the polynucleotide) is between about 10:1 to about 50:1, inclusive. In certain embodiments, the nitrogen phosphate ratio is between about 10:1 to about 45:1, between about 15:1 to about 45:1, or between about 20:1 to about 40:1, inclusive. In certain embodiments, the APPL:polynucleotide mass ratio is between about 10:1 to about 20: l, inclusive. In certain embodiments, the APPL:polynucleotide mass ratio is about 15:1. In certain ments, the olynucleotide molar ratio is between about 10:1 to about 400:1, inclusive. In n embodiments, the APPL:polynucleotide molar ratio is between about 10:1 to about 350:1, between about 15:1 to about 300:1, or between about 20:1 to about 250:1, inclusive.

In certain embodiments, the complex may form a particle. In certain embodiments, the diameter of the particles ranges from 10—500 micrometers. In certain ments, the diameter of the particles ranges from 10— 1200 micrometers. In certain embodiments, the er of the particles ranges from 50— 150 micrometers. In certain embodiments, the diameter of the particles ranges from 10—500 nm, in certain embodiments the diameter of the particles ranges from 10—1200 nm, and in certain embodimentsfrom 50— WO 63468 150 nm. The particles may be associated with a targeting agent as described below. In certain embodiments, the diameter of the particles ranges from 10—500 pm, in certain embodimentsthe diameter of the particles ranges from 10—1200 pm, and in certain embodimentsfrom 50—150 pm. The particles may be associated with a targeting agent as described below. The film ecture is precisely designed and can be controlled to 1 nm precision with a range from 1 to 150000 nm and with a definite knowledge of its molecular composition.

The polynucleotide may be complexed, ulated by an APPL, or included in a composition comprising an APPL. The polynucleotide may be any nucleic acid including, but not limited to, RNA and DNA. In certain embodiments, the polynucleotide is DNA. In certain ments, the polynucleotide is RNA. In n ments, upon delivery of the RNA into a cell, the RNA is able to interfere with the expression of a specific gene in the biological cell.

In certain embodiments, the polynucleotide is an RNA that carries out RNA interference (RNAi). The phenomenon of RNAi is discussed in greater , for example, in the following references: Elbashir et al., 2001, Genes Dev., 15: 188; Fire et al., 1998, , 391:806; Tabara et al., 1999, Cell, 99:123; Hammond et al., Nature, 2000, 404:293; Zamore et al., 2000, Cell, 101:25; Chakraborty, 2007, Curr. Drug Targets, 8:469; and Morris and Rossi, 2006, Gene Ther, 13:553. In certain embodiments, the polynucleotide is a dsRNA (double—stranded RNA). In certain embodiments, the polynucleotide is an siRNA (short ering RNA). In certain ments, the polynucleotide is an shRNA (short hairpin RNA). In certain embodiments, the polynucleotide is an miRNA (micro RNA). Micro RNAs (miRNAs) are genomically encoded non—coding RNAs of about 21 — 23 nucleotides in length that help regulate gene expression, particularly during development. See, e. g., Bartel, 2004, Cell, 116:281; Novina and Sharp, 2004, Nature, 430: 161; and US. Patent Publication 2005/0059005; also reviewed in Wang and Li, 2007, Front. Biosci., 12:3975; and Zhao, 2007, Trends Biochem. Sci., 32: 189. In certain embodiments, the polynucleotide is an antisense RNA.

In certain embodiments, the polynucleotide may be provided as an antisense agent or RNA interference (RNAi). See, e.g., Fire et al., Nature 391:806—81 1, 1998.

Antisense therapy is meant to include, e. g., administration or in situ provision of single— or double—stranded oligonucleotides or their derivatives which specifically ize, e. g., bind, under cellular conditions, with cellular mRNA and/or genomic DNA, or mutants thereof, so as to t expression of the encoded protein, e.g., by inhibiting transcription and/or translation. See, e. g., Crooke “Molecular mechanisms of action of antisense drugs” m.

Biophys. Acta l489(l):31—44, 1999; Crooke “Evaluating the mechanism of action of antiproliferative antisense drugs” Antisense Nucleic Acid Drug Dev. 10(2): 123— 126, discussion 127, 2000; Methods in Enzymology volumes 313—314, 1999. The binding may be by tional base pair complementarity, or, for example, in the case of binding to DNA duplexes, through specific interactions in the major groove of the double helix (i.e., triple helix ion). See, e.g., Chan et al., J. Mol. Med. 75(4):267-282, 1997.

In some embodiments, dsRNA, siRNA, shRNA, miRNA, antisense RNA, and/or RNAi can be designed and/or predicted using one or more of a large number of available thms. To give but a few examples, the following resources can be utilized to design and/or t polynucleotides: thms found at Alnylum Online, con Online, OligoEngine Online, Molecula Online, Ambion Online, BioPredsi Online, RNAi Web Online, Chang Bioscience Online, Invitrogen Online, LentiWeb Online GenScript Online, Protocol Online; Reynolds et al., 2004, Nat. Biotechnol, 22:326; Naito et al., 2006, Nucleic Acids Res., 34:W448; Li et al., 2007, RNA, 13:1765; Yiu et al., 2005, Bioinformatics, 21:144; and Jia et al., 2006, BMC Bioinformatics, 7: 271.

The polynucleotides may be of any size or sequence, and they may be single— or double—stranded. In certain embodiments, the polynucleotide is greater than 100 base pairs long. In n embodiments, the polynucleotide is greater than 1000 base pairs long and may be greater than 10,000 base pairs long. The polynucleotide is optionally purified and substantially pure. In certain ments, the polynucleotide is greater than 50% pure, in certain embodiments greater than 75% pure, and in certain embodimentsgreater than 95% pure. The polynucleotide may be provided by any means known in the art. In certain embodiments, the polynucleotide has been engineered using recombinant techniques. See, e.g., l et al., Current Protocols in Molecular Biology (John Wiley & Sons, Inc., New York, 1999); Molecular Cloning: A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch, and Maniatis (Cold Spring Harbor tory Press: 1989). The polynucleotide may also be obtained from natural sources and purified from inating components found normally in nature. The polynucleotide may also be chemically synthesized in a laboratory. In certain embodiments, the polynucleotide is synthesized using standard solid phase chemistry.

The polynucleotide may be modified by chemical or biological means. In n embodiments, these cations lead to increased stability of the polynucleotide.

Modifications include ation, phosphorylation, end—capping, etc.

WO 63468 Derivatives of polynucleotides may also be used in the present invention.

These tives include modifications in the bases, sugars, and/or phosphate es of the polynucleotide. Modified bases include, but are not limited to, those found in the following nucleoside s: 2—aminoadenosine, 2—thiothymidine, inosine, pyrrolo—pyrimidine, 3— methyl adenosine, 5—methylcytidine, C5—bromouridine, CS—fluorouridine, CS—iodouridine, pynyl—uridine, C5—propynyl—cytidine, C5—methylcytidine, 7—deazaadenosine, 7—deazaguanosine, 8—oxoadenosine, 8—oxoguanosine, O(6)—methylguanine, and 2—thiocytidine. ed sugars include, but are not limited to, 2’—fluororibose, ribose, 2’—deoxyribose, 3’— 2’,3”—dideoxyribose, 2’,3’—dideoxyribose, arabinose (the 2’—epimer of ribose), acyclic sugars, and hexoses. The nucleosides may be strung together by linkages other than the phosphodiester linkage found in naturally occurring DNA and RNA. Modified linkages include, but are not limited to, phosphorothioate and 5’—N—phosphoramidite linkages.

Combinations of the various modifications may be used in a single polynucleotide. These modified cleotides may be provided by any means known in the art; however, as will be appreciated by those of skill in this art, the modified polynucleotides may be ed using synthetic chemistry in vitro.

The polynucleotides to be delivered may be in any form. For example, the polynucleotide may be a circular plasmid, a linearized plasmid, a cosmid, a viral genome, a modified viral genome, an cial chromosome, etc.

The polynucleotide may be of any sequence. In certain embodiments, the polynucleotide encodes a protein or peptide. The encoded proteins may be enzymes, structural proteins, receptors, soluble receptors, ion channels, pharmaceutically active ns, cytokines, interleukins, antibodies, antibody fragments, antigens, coagulation factors, n, growth factors, hormones, insulin, etc. The polynucleotide may also comprise tory regions to control the expression of a gene. These regulatory regions may include, but are not limited to, promoters, enhancer elements, repressor ts, TATA box, ribosomal binding sites, stop site for transcription, etc. In certain ments, the polynucleotide is not intended to encode a protein. For example, the cleotide may be used to fix an error in the genome of the cell being transfected.

In certain embodiments, the polynucleotide to be delivered comprises a sequence encoding an antigenic peptide or protein. Nanoparticles containing these polynucleotides can be delivered to an individual to induce an immunologic response sufficient to decrease the chance of a subsequent infection and/or lessen the ms associated with such an infection. The polynucleotide of these vaccines may be combined with interleukins, eron, cytokines, and adjuvants such as cholera toxin, alum, Freund’s adjuvant, etc. A large number of adjuvant compounds are known; a useful compendium of many such nds is prepared by the National Institutes of Health. See, e. g., Allison Dev. Biol. Stand. 92:3—11, 1998; Unkeless et al., Annu. Rev. Immunol. 6:251—281, 1998; and Phillips et al., Vaccine 10:151—158, 1992.

The antigenic protein or peptides encoded by the polynucleotide may be derived from such bacterial organisms as Streptococccus niae, hilus influenzae, Staphylococcus aureus, Streptococcus pyrogenes, Corynebacterium diphtheriae, Listeria monocytogenes, us anthracis, idium tetani, Clostridium botulinum, Clostridium perfringens, ria meningitidis, Neisseria gonorrhoeae, Streptococcus mutans, Pseudomonas aeruginosa, Salmonella typhi, Haemopliilus parainfluenzae, Bordetella pertussis, Francisella nsis, Yersinia pestis, Vibrio cholerae, Legionella pneumophila, Mycobacterium tuberculosis, Mycobacterium leprae, Treponema pallidum, Leptospirosis interrogans, ia burgdorferi, Campliylobacterjejuni, and the like; from such viruses as smallpox, influenza A and B, respiratory syncytial virus, parainfluenza, measles, HIV, varicella—zoster, herpes simplex 1 and 2, cytomegalovirus, Epstein—Barr virus, rotavirus, rhinovirus, adenovirus, papillomavirus, poliovirus, mumps, rabies, rubella, coxsackieviruses, equine encephalitis, Japanese encephalitis, yellow fever, Rift Valley fever, hepatitis A, B, C, D, and E virus, and the like; and from such fungal, protozoan, and tic organisms such as Cryptococcus neoformans, Histoplasma capsulatum, Candida albicans, Candida tropicalis, Nocardia asteroides, Rickettsia ricketsii, Rickettsia typhi, Mycoplasma pneumoniae, Chlamydial psittaci, Chlamydial trachomatis, Plasmodiumfalciparum, Trypanosoma , Entamoeba histolytica, Toxoplasma gondii, Trichomonas vaginalis, Schistosoma mansoni, and the like.

Particles The present invention also plates APPLs useful as a delivery device.

APPLs have several properties that make them particularly le for delivery, including: 1) the ability of an APPL to complex and “protect” labile agents; 2) the ability to buffer the pH in the endosome; 3) the ability to act as a “proton sponge” and cause endosomolysis; and 4) the ability to neutralize the charge on negatively charged agents.

In certain embodiments, an APPL is used to form particles containing the agent to be delivered. An APPL may be used to ulate agents including, but not limited to, organic les (e.g., cholesterol, , inorganic les, nucleic acids, proteins, peptides, polynucleotides, targeting agents, isotopically labeled organic or inorganic molecules, vaccines, immunological , etc. Other exemplary agents are described in greater detail herein. These particles may include other materials such as polymers (e.g., synthetic polymers (e.g., PEG, PLGA), natural polymers (e.g., phospholipids)). In certain embodiments, the APPL is mixed with one or more agents (e.g., cholesterol) and/or one or more other als (e.g., polymers).

] In certain embodiments, the diameter of the particles range from between 1 micrometer to 1,000 eters. In certain embodiments, the diameter of the particles range from between from 1 micrometer to 100 micrometers. In certain embodiments, the diameter of the particles range from between from 1 micrometer to 10 micrometers. In certain embodiments, the diameter of the particles range from between from 10 micrometer to 100 micrometers. In certain embodiments, the diameter of the particles range from between from 100 micrometer to 1,000 micrometers. In n embodiments, the les range from l—5 micrometers. In certain embodiments, the diameter of the les range from between 1 nm to 1,000 nm. In certain embodiments, the er of the les range from between from 1 nm to 100 nm. In certain embodiments, the diameter of the particles range from between from 1 nm to 10 nm. In certain embodiments, the diameter of the particles range from between from 10 nm to 100 nm. In certain ments, the diameter of the particles range from between from 100 nm to 1,000 nm. In certain embodiments, the particles range from l—5 nm. In certain embodiments, the diameter of the particles range from between 1 pm to 1,000 pm. In certain embodiments, the diameter of the particles range from between from 1 pm to 100 pm. In certain embodiments, the diameter of the particles range from between from 1 pm to 10 pm. In n ments, the diameter of the particles range from between from 10 pm to 100 pm. In certain embodiments, the diameter of the particles range from n from 100 pm to 1,000 pm. In n embodiments, the particles range from 1— pm.

The particles may be prepared using any method known in this art. These include, but are not limited to, spray drying, single and double emulsion solvent ation, solvent extraction, phase separation, simple and complex coacervation, and other methods well known to those of ordinary skill in the art. In certain embodiments, methods of preparing the particles are the double emulsion process and spray drying. The conditions used in ing the particles may be altered to yield particles of a desired size or property (e.g., hydrophobicity, hydrophilicity, external logy, “stickiness”, shape, etc). The method of preparing the particle and the conditions (e.g., solvent, temperature, concentration, air flow rate, etc.) used may also depend on the agent being encapsulated and/or the composition of the matrix.

Methods developed for making particles for delivery of encapsulated agents are bed in the ture. See, e. g., Doubrow, M., Ed., “Microcapsules and Nanoparticles in Medicine and Pharmacy,” CRC Press, Boca Raton, 1992; witz and Langer, J.

Controlled Release 5:13—22, 1987; Mathiowitz et al., Reactive Polymers 6:275-283, 1987; Mathiowitz et al., J. Appl. Polymer Sci. 35:755—774, 1988.

If the particles prepared by any of the above methods have a size range outside of the desired range, the les can be sized, for example, using a sieve. The particle may also be . In certain embodiments, the particles are coated with a targeting agent. In other embodiments, the particles are coated to achieve desirable surface properties (e.g., a particular charge).

Micelles and Liposomes The present invention further contemplates use of APPLs in the preparation of micelles or liposomes. Any agent may be further included in a micelle or liposome. Micelles and liposomes are particularly useful in delivering hydrophobic agents such as hydrophobic small molecules. When the micelle or liposome is complexed with (e.g., encapsulates or covers) a polynucleotide it is also ed to as a “lipoplex.” Many techniques for preparing micelle and liposomes are known in the art, and any such method may be used with an APPL to make micelles and liposomes.

In certain embodiments, liposomes are formed through spontaneous assembly.

In other embodiments, liposomes are formed when thin lipid films or lipid cakes are hydrated and stacks of lipid crystalline bilayers become fluid and swell. The hydrated lipid sheets detach during agitation and lose to form large, multilamellar vesicles (LMV). This ts interaction of water with the hydrocarbon core of the bilayers at the edges. Once these particles have formed, reducing the size of the particle can be modified through input of sonic energy (sonication) or mechanical energy (extrusion). See, e. g., Walde, P. “Preparation of Vesicles (Liposomes)” In pedia ofNanoscience and chnology; Nalwa, H. S.

Ed. American Scientific Publishers: Los Angeles, 2004; Vol. 9, pp. 43-79; Szoka et al., “Comparative ties and Methods of Preparation of Lipid Vesicles (Liposomes)” Ann.

Rev. Biophys. Bioeng. 9:467—508, 1980; each of which is incorporated herein. The ation of lipsomes es preparing the APPL for hydration, hydrating the APPL with agitation, and sizing the vesicles to achieve a nous bution of liposomes. APPLs are first dissolved in an organic solvent to assure a homogeneous mixture of the APPL. The solvent is then removed to form a polymer—derived film. This polymer—derived film is ghly dried to remove residual organic solvent by placing the vial or flask on a vaccuum pump overnight. Hydration of the polymer—derived film is accomplished by adding an aqueous medium and ing the mixture. Disruption of LMV suspensions using sonic energy typically produces small unilamellar vesicles (SUV) with diameters in the range of —50 nm. Lipid extrusion is a technique in which a lipid/polymer suspension is forced through a polycarbonate filter with a d pore size to yield particles having a diameter near the pore size of the filter used. Extrusion through filters with 100 nm pores typically yields large, unilamellar polymer—derived vesicles (LUV) with a mean diameter of 120—140 nm. In certain embodiments, the amount of APPL in the liposome ranges from 30—80 mol%, in certain embodiments40—70 mol%, and in certain embodiments 60—70 mol%. In certain embodiments, the APPL employed further complexes an agent, such as DNA and RNA. In such embodiments, the application of the liposome is the delivery of polynucleotides.

The following scientific papers bed other methods for ing liposomes and es: Narang et al., nic Lipids with Increased DNA Binding Affinity for al Gene Transfer in Dividing and Nondividing Cells” Bioconjugate Chem. 16: 156—68, 2005; Hofland et al., “Formation of stable cationic lipid/DNA xes for gene transfer” Proc. Natl. Acad. Sci. USA 93:7305—7309, July 1996; Byk et al., esis, Activity, and Structure—Activity Relationship Studies of Novel Cationic Lipids for DNA er” J. Med. Chem. 41(2):224—235, 1998; Wu et al., “Cationic Lipid Polymerization as a Novel Approach for Constructing New DNA Delivery Agents” Bioconjugate Chem. 12:251— 57, 2001; Lukyanov et al., “Micelles from lipid derivatives of soluble polymers as delivery systems for poorly soluble drugs” Advanced Drug Delivery Reviews 56:1273—1289, 2004; Tranchant et al., “Physicochemical optimisation of plasmid delivery by cationic lipids” J. Gene Med. 6:S24—S35, 2004; van Balen et al., “Liposome/Water Lipophilicity: Methods, ation Content, and Pharmaceutical Applications” Medicinal Research Rev. 24(3):299- 324, 2004.

Treatment Methods ] It is estimated that over 10,000 human diseases are caused by genetic disorders, which are abnormalities in genes or chromosomes. See, e.g., McClellan, J. and MC. King, Genetic heterogeneity in human disease. Cell. 141(2): p. 210—7; an, S.A., et al., Therapeutic siRNAs for dominant genetic skin disorders including pachyonychia congenita. J Derrnatol Sci, 2008. 51(3): p. 151—7. Many of these diseases are fatal, such as cancer, severe hypercholesterolemia, and familial amyloidotic polyneuropathy. See, e.g., Frank— Kamenetsky, M., et al., eutic RNAi targeting PCSK9 acutely lowers plasma cholesterol in rodents and LDL cholesterol in nonhuman primates. Proc Natl Acad Sci U S A, 2008. 105(33): p. 11915—20; Coelho, T., Familial amyloid polyneuropathy: new pments in genetics and treatment. Curr Opin Neurol, 1996. 9(5): p. 355—9. Since the discovery of gene sion silencing via RNA interference (RNAi) by Fire and Mello (Fire, A., et al., Potent and specific genetic interference by -stranded RNA in Caenorhabditis elegans. , 1998. 391(6669): p. 806—1 1), there has been extensive effort toward ping therapeutic applications for RNAi in humans. See, e.g., Davis, M.E., The first targeted delivery ofsiRNA in humans via a self-assembling, cyclodextrin polymer-based nanoparticle: from concept to clinic. Mol Pharm, 2009. 6(3): p. 659—68; Whitehead, K.A., R.

Langer, and D.G. Anderson, Knocking down barriers: advances in siRNA ry. Nat. Rev.

Drug Discovery, 2009. 8(2): p. 129—138; Tan, S.J., et al., Engineering Nanocarriers for siRNA Delivery. Small. 7(7): p. ; Castanotto, D. and J .J . Rossi, The promises and pitfalls ofRNA-interference-based therapeutics. Nature, 2009. 457(7228): p. 426—33; Chen, Y. and L. Huang, Tumor-targeted ry of siRNA by non-viral vector: safe and ejfective cancer therapy. Expert Opin Drug Deliv, 2008. 5(12): p. 1301—1 1; Weinstein, S. and D. Peer, RNAi nanomedicines: challenges and opportunities within the immune system.

Nanotechnology. 21(23): p. 232001; Fenske, DB. and PR. Cullis, Liposomal nanomedicines.

Expert Opin Drug Deliv, 2008. 5(1): p. 25—44; and Thiel, K.W. and RH. Giangrande, Therapeutic ations ofDNA and RNA rs. Oligonucleotides, 2009. 19(3): p. 209— 22. Currently, there are more than 20 clinical trials ongoing or completed involving siRNA therapeutics, which have shown promising results for the treatment of various diseases. See, e.g., Burnett, J .C., J .J . Rossi, and K. Tiemann, Current ss of siRNA/shRNA therapeutics in clinical trials. Biotechnol J. 6(9): p. 6. However, the efficient and safe ry of siRNA is still a key challenge in the development of siRNA therapeutics. See, e. g., Juliano, R., et al., Biological barriers to therapy with antisense and siRNA oligonucleotides.

Mol Pharm, 2009. 6(3): p. 686—95.

Thus, in another aspect, ed are methods of using APPLs, e. g., for the treatment of a disease, disorder or condition from which a subject suffers. It is contemplated that APPLs will be useful in the treatment of a variety of diseases, disorders, or conditions, especially a system for delivering agents useful in the treatment of that particular disease, disorder, or condition. “Disease,” “disorder,” and “condition” are used interchangeably herein. In certain embodiments, the disease, disorder or condition from which a subject suffers is caused by an abnormality in a gene or chromosome of the subject.

For example, in one embodiment, provided is a method of treating disease, disorder, or condition from which a subject suffers, comprising administering to a subject in need thereof an effective amount of a composition comprising an APPL, or salt thereof.

Exemplary disease, er, or conditions plated include, but are not limited to, proliferative disorders, inflammatory disorders, autoimmune disorders, painful conditions, liver diseases, and amyloid neuropathies.

As used herein, an “active ingredient” is any agent which elicits the desired biological response. For example, the APPL may be the active ient in the composition.

Other agents, e.g., therapeutic , as described herein may also be classified as an active ient. In certain embodiments, the composition further comprises, in on to the APPL, a therapeutic agent useful in treating the disease, disorder, or condition. In n embodiments, the APPL encapsulates the other peutic) agent. In certain ments, the APPL and the other (therapeutic) agent form a le (e.g., a nanoparticle, a microparticle, a micelle, a liposome, a lipoplex).

In certain embodiments, the condition is a proliferative disorder and, in certain embodiments, the composition further es an anti—cancer agent. Exemplary proliferative diseases include, but are not limited to, tumors, begnin neoplasms, pre—malignant neoplasms (carcinoma in situ), and malignanat neoplasms (cancers).

Exemplary cancers e, but are not limited to, ic neuroma, adenocarcinoma, adrenal gland cancer, anal cancer, angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma), ix cancer, benign onal gammopathy, biliary cancer (e.g., cholangiocarcinoma), bladder cancer, breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast), brain cancer (e.g., meningioma; glioma, e.g., ytoma, oligodendroglioma; medulloblastoma), bronchus cancer, carcinoid tumor, cervical cancer (e.g., al adenocarcinoma), choriocarcinoma, chordoma, craniopharyngioma, colorectal cancer (e.g., colon cancer, rectal cancer, ctal adenocarcinoma), lial carcinoma, ependymoma, endotheliosarcoma (e.g., Kaposi’s sarcoma, multiple idiopathic hemorrhagic sarcoma), endometrial cancer (e.g., uterine cancer, uterine sarcoma), esophageal cancer (e.g., arcinoma of the esophagus, Barrett’s adenocarinoma), Ewing’s sarcoma, eye cancer (e.g., intraocular melanoma, retinoblastoma), familiar hypereosinophilia, gall bladder cancer, gastric cancer (e.g., stomach adenocarcinoma), gastrointestinal stromal tumor (GIST), head 2012/062222 and neck cancer (e.g., head and neck squamous cell oma, oral cancer (e.g., oral squamous cell carcinoma (OSCC), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)), hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia (ALL) (e.g., B—cell ALL, T—cell ALL), acute myelocytic leukemia (AML) (e.g., B—cell AML, T—cell AML), chronic myelocytic leukemia (CML) (e.g., B—cell CML, T—cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B—cell CLL, T—cell CLL); lymphoma such as Hodgkin lymphoma (HL) (e.g., B—cell HL, T—cell HL) and dgkin lymphoma (NHL) (e.g., B—cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B—cell lymphoma (DLBCL)), follicular lymphoma, c lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B—cell lymphomas (e.g., mucosa—associated lymphoid tissue (MALT) lymphomas, nodal marginal zone B—cell lymphoma, splenic marginal zone B—cell ma), primary mediastinal B—cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma (i.e., “Waldenstrom's macroglobulinemia”), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B—lymphoblastic ma and primary central nervous system (CNS) ma; and T—cell NHL such as precursor T— lymphoblastic lymphoma/leukemia, peripheral T—cell lymphoma (PTCL) (e.g., cutaneous T— cell lymphoma (CTCL) (e.g., mycosis fungiodes, Sezary syndrome), angioimmunoblastic T— cell lymphoma, extranodal natural killer T—cell lymphoma, enteropathy type T—cell ma, subcutaneous panniculitis—like T—cell lymphoma, anaplastic large cell lymphoma); a e of one or more leukemia/lymphoma as described above; and multiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease), hemangioblastoma, inflammatory myofibroblastic tumors, cytic amyloidosis, kidney cancer (e.g., nephroblastoma aka. Wilms’ tumor, renal cell carcinoma), liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma), lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non—small cell lung cancer (NSCLC), adenocarcinoma of the lung), leiomyosarcoma (LMS), mastocytosis (e.g., systemic mastocytosis), myelodysplastic syndrome (MDS), mesothelioma, myeloproliferative disorder (MPD) (e.g., polycythemia Vera (PV), essential thrombocytosis (ET), nic myeloid metaplasia (AMM) a. k.a. myelofibrosis (MF), chronic idiopathic ibrosis, chronic myelocytic leukemia (CML), c neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)), lastoma, neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis), neuroendocrine cancer (e.g., gastroenteropancreatic ndoctrine tumor (GEP—NET), carcinoid tumor), osteosarcoma, ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma), papillary adenocarcinoma, pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (lPMN), Islet cell tumors), penile cancer (e.g., Paget’s disease of the penis and m), pinealoma, primitive neuroectodermal tumor (PNT), prostate cancer (e.g., prostate adenocarcinoma), rectal cancer, rhabdomyosarcoma, salivary gland cancer, skin cancer (e.g., squamous cell carcinoma (SCC), acanthoma (KA), melanoma, basal cell carcinoma (BCC)), small bowel cancer (e.g., ix cancer), soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant eral nerve sheath tumor (MPNST), osarcoma, fibrosarcoma, myxosarcoma), sebaceous gland carcinoma, sweat gland carcinoma, synovioma, testicular cancer (e.g., seminoma, testicular embryonal carcinoma), thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid ), urethral cancer, vaginal cancer and vulvar cancer (e.g., Paget’s e of the vulva).

Anti—cancer agents encompass biotherapeutic anti—cancer agents as well as herapeutic agents.

Exemplary biotherapeutic anti—cancer agents include, but are not limited to, erons, cytokines (e.g., tumor necrosis factor, interferon 0t, interferon y), vaccines, hematopoietic growth factors, monoclonal erapy, immunostimulants and/or immunodulatory agents (e.g., IL—l, 2, 4, 6, or 12), immune cell growth factors (e.g., GM— CSF) and antibodies (e.g. HERCEPTIN (trastuzumab), T—DMl, AVASTIN (bevacizumab), X (cetuximab), VECTIBIX (panitumumab), RITUXAN (rituximab), BEXXAR (tositumomab)).

Exemplary chemotherapeutic agents include, but are not limited to, anti— estrogens (e.g. tamoxifen, fene, and megestrol), LHRH ts (e.g. goscrclin and leuprolide), anti—androgens (e.g. de and tamide), photodynamic therapies (e.g. vertoporfin A), phthalocyanine, photosensitizer Pc4, and demethoxy—hypocrellin A (2BA—2—DMHA)), nitrogen mustards (e.g. cyclophosphamide, ifosfamide, trofosfamide, chlorambucil, estramustine, and melphalan), nitrosoureas (e.g. carmustine (BCNU) and lomustine (CCNU)), alkylsulphonates (e.g. busulfan and treosulfan), triazenes (e.g. dacarbazine, temozolomide), platinum containing compounds (e.g. cisplatin, carboplatin, oxaliplatin), vinca alkaloids (e.g. vincristine, vinblastine, vindesine, and vinorelbine), taxoids (e.g. paclitaxel or a paclitaxel equivalent such as rticle albumin—bound axel (ABRAXANE), docosahexaenoic acid bound—paclitaxel (DHA—paclitaxel, Taxoprexin), polyglutamate bound—paclitaxel (PG—paclitaxel, paclitaxel poliglumex, CT— 2103, XYOTAX), the tumor—activated prodrug (TAP) ANG1005 (Angiopep—2 bound to three molecules of paclitaxel), paclitaxel—EC—l (paclitaxel bound to the erbB2—recognizing peptide EC—l), and e—conjugated paclitaxel, e.g., 2'—paclitaxel methyl 2—glucopyranosyl succinate; docetaxel, taxol), epipodophyllins (e.g. etoposide, etoposide ate, teniposide, topotecan, 9—aminocamptothecin, camptoirinotecan, irinotecan, crisnatol, mytomycin C), anti—metabolites, DHFR inhibitors (e.g. methotrexate, dichloromethotrexate, trimetrexate, edatrexate), IMP dehydrogenase inhibitors (e.g. enolic acid, tiazofurin, ribaVirin, and EICAR), clotide reductase inhibitors (e.g. hydroxyurea and deferoxamine), uracil analogs (e.g. S—fluorouracil (S—FU), floxuridine, doxifluridine, ratitrexed, tegafur—uracil, capecitabine), cytosine analogs (e.g. cytarabine (ara C), cytosine arabinoside, and fludarabine), purine analogs (e.g. mercaptopurine and Thioguanine), Vitamin D3 analogs (e.g. EB 1089, CB 1093, and KH 1060), isoprenylation inhibitors (e.g. lovastatin), dopaminergic neurotoxins (e.g. 1—methyl—4—phenylpyridinium ion), cell cycle inhibitors (e.g. staurosporine), actinomycin (e.g. actinomycin D, dactinomycin), bleomycin (e.g. bleomycin A2, bleomycin B2, ycin), anthracycline (e.g. daunorubicin, bicin, pegylated liposomal doxorubicin, idarubicin, epirubicin, pirarubicin, zorubicin, mitoxantrone), MDR inhibitors (e.g. verapamil), Ca2+ ATPase inhibitors (e.g. thapsigargin), imatinib, omide, lenalidomide, ne kinase inhibitors (e.g., aXitinib (AG013736), bosutinib (SKI—606), cediranib (RECENTINTM, AZD2171), dasatinib (SPRYCEL®, BMS—354825), erlotinib (TARCEVA®), nib (IRESSA®), imatinib (Gleevec®, CGP57148B, STI—571), lapatinib (TYKERB®, TYVERB®), lestaurtinib 01), neratinib (HKI—272), nilotinib NA®), semaxanib (semaXinib, SU5416), sunitinib (SUTENT®, SU11248), toceranib (PALLADIA®), vandetanib (ZACT]MA®, ZD6474), vatalanib (PTK787, PTK/ZK), trastuzumab (HERCEPTIN®), bevacizumab (AVASTIN®), rituXimab AN®), cetuXimab (ERBITUX®), panitumumab (VECTIBIX®), ranibizumab (Lucentis®), nilotinib (TASIGNA®), sorafenib (NEXAVAR®), everolimus (AFINITOR®), alemtuzumab (CAMPATH®), gemtuzumab ozogamicin (MYLOTARG®), temsirolimus (TORISEL®), ENMD-2076, PCI—32765, AC220, nib lactate (TKI258, CHIR-258), BIBW 2992 (TOVOKTM), SGX523, PF—04217903, PF-02341066, PF-299804, 7607, ABT-869, MP470, BIBF 1120 (VARGATEF®), 4, JNJ-26483327, 5, DCC—2036, EMS-690154, 981, tivozanib (AV-951), OSI—930, MM-121, XL—184, XL-647, and/or XL228), proteasome inhibitors (e.g., bortezomib (VELCADE)), mTOR inhibitors (e.g., rapamycin, temsirolimus 79), everolimus (RAD—001), ridaforolimus, AP23573 ), AZD8055 (AstraZeneca), BEZ235 (Novartis), BGT226 (Norvartis), XL765 (Sanofi WO 63468 Aventis), PF—4691502 (Pfizer), 0 (Genetech), SF1126 (Semafoe) and 081—027 (081)), oblimersen, gemcitabine, omycin, leucovorin, pemetrexed, cyclophosphamide, dacarbazine, procarbizine, prednisolone, dexamethasone, campathecin, plicamycin, asparaginase, aminopterin, terin, porfiromycin, melphalan, leurosidine, leurosine, chlorambucil, trabectedin, bazine, discodermolide, carminomycin,, terin, and thyl melamine.

In certain embodiments, the ion is an inflammatory disorder and, in certain embodiments, the composition further includes an anti—inflammatory agent. The term “inflammatory disorder” refers to those diseases, disorders or conditions that are characterized by signs of pain (dolor, from the tion of noxious substances and the stimulation of nerves), heat (calor, from vasodilatation), redness (rubor, from vasodilatation and increased blood flow), swelling (tumor, from excessive inflow or restricted outflow of fluid), and/or loss of function (functio laesa, which can be partial or complete, temporary or permanent. Inflammation takes on many forms and includes, but is not limited to, acute, ve, atrophic, catarrhal, chronic, cirrhotic, e, inated, exudative, fibrinous, fibrosing, focal, granulomatous, hyperplastic, hypertrophic, interstitial, metastatic, necrotic, obliterative, parenchymatous, plastic, productive, proliferous, pseudomembranous, purulent, sclerosing, seroplastic, serous, simple, specific, subacute, suppurative, toxic, traumatic, and/or ulcerative inflammation.

Exemplary inflammatory disorders include, but are not limited to, inflammation associated with acne, anemia (e.g., aplastic anemia, ytic autoimmune anaemia), asthma, arteritis (e.g., teritis, temporal arteritis, periarteritis nodosa, Takayasu’s arteritis), tis (e.g., crystalline arthritis, osteoarthritis, psoriatic arthritis, gouty arthritis, reactive arthritis, rheumatoid arthritis and Reiter’s arthritis), ankylosing spondylitis, amylosis, ophic lateral sclerosis, autoimmune diseases, allergies or ic reactions, atherosclerosis, bronchitis, bursitis, chronic prostatitis, conjunctivitis, Chagas disease, chronic obstructive pulmonary disease, cermatomyositis, diverticulitis, diabetes (e.g., type I diabetes us, type 2 diabetes mellitus), a skin condition (e.g., psoriasis, eczema, burns, dermatitis, pruritus (itch)), endometriosis, Guillain—Barre syndrome, infection, ischaemic heart disease, Kawasaki disease, glomerulonephritis, gingivitis, hypersensitivity, headaches (e.g., migraine headaches, tension headaches), ileus (e.g., postoperative ileus and ileus during sepsis), idiopathic thrombocytopenic purpura, interstitial cystitis ul bladder syndrome), gastrointestinal disorder (e.g. , selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic gastrointestinal disorders (e.g., eosinophilic esophagitis, eosinophilic gastritis, eosinophilic gastroenteritis, philic colitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, or its synonym GERD), inflammatory bowel disease (IBD) (e.g., Crohn’s disease, ulcerative colitis, enous colitis, lymphocytic colitis, ischaemic colitis, diversion colitis, Behcet’s syndrome, indeterminate colitis) and inflammatory bowel syndrome (IBS)), lupus, multiple sclerosis, a, myeasthenia gravis, myocardial ischemia, nephrotic syndrome, pemphigus vulgaris, pernicious aneaemia, peptic ulcers, ositis, primary biliary cirrhosis, neuroinflammation associated with brain ers (e.g., Parkinson’s e, Huntington’s disease, and Alzheimer’s disease), prostatitis, chronic inflammation associated with cranial ion injury, pelvic inflammatory disease, reperfusion injury, regional enteritis, rheumatic fever, systemic lupus erythematosus, schleroderma, scierodoma, sarcoidosis, spondyloarthopathies, Sjogren’s syndrome, thyroiditis, transplantation rejection, tendonitis, trauma or injury (e.g., frostbite, chemical nts, toxins, scarring, burns, physical injury), vasculitis, vitiligo and Wegener’s granulomatosis.

In certain embodiments, the inflammatory disorder is inflammation associated with a proliferative disorder, e.g., inflammation associated with cancer.

In certain ments, the condition is an autoimmune disorder and, in certain embodiments, the ition further includes an immunomodulatory agent. Exemplary mune disorders include, but are not limited to, arthritis (including rheumatoid arthritis, spondyloarthopathies, gouty arthritis, degenerative joint diseases such as osteoarthritis, systemic lupus matosus, Sjogren's syndrome, ankylosing spondylitis, undifferentiated litis, Behcet's disease, haemolytic autoimmune anaemias, multiple sis, amyotrophic lateral sclerosis, amylosis, acute painful shoulder, psoriatic, and juvenile arthritis), asthma, atherosclerosis, orosis, bronchitis, tendonitis, bursitis, skin condition (e.g., psoriasis, eczema, burns, dermatitis, pruritus (itch)), enuresis, eosinophilic disease, gastrointestinal disorder (e.g. , selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic gastrointestinal ers (e.g., eosinophilic esophagitis, eosinophilic gastritis, eosinophilic gastroenteritis, eosinophilic colitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, or its m GERD), inflammatory bowel disease (IBD) (e.g., Crohn's disease, ulcerative colitis, collagenous s, lymphocytic colitis, ischaemic colitis, diversion colitis, Behcet's syndrome, indeterminate colitis) and inflammatory bowel syndrome (IBS)), and disorders ameliorated by a gastroprokinetic agent (e.g., ileus, postoperative ileus and ileus during sepsis; esophageal reflux disease (GORD, or its synonym GERD); philic gitis, gastroparesis such as diabetic WO 63468 2012/062222 gastroparesis; food intolerances and food allergies and other functional bowel disorders, such as non—ulcerative dyspepsia (NUD) and rdiac chest pain (NCCP, including costo— chondritis)).

In certain embodiments, the condition is a painful ion and, in certain embodiments, the composition further includes an analgesic agent. A “painful condition” includes, but is not limited to, neuropathic pain (e.g., peripheral neuropathic pain), central pain, deafferentiation pain, chronic pain (e.g., chronic nociceptive pain, and other forms of chronic pain such as perative pain, e.g., pain g after hip, knee, or other replacement surgery), pre —operative pain, stimulus of nociceptive receptors (nociceptive pain), acute pain (e.g. , phantom and transient acute pain), noninflammatory pain, atory pain, pain associated with cancer, wound pain, burn pain, postoperative pain, pain associated with medical procedures, pain resulting from pruritus, painful r syndrome, pain associated with premenstrual dysphoric er and/or strual syndrome, pain associated with chronic fatigue syndrome, pain associated with pre—terrn labor, pain associated with withdrawl symptoms from drug addiction, joint pain, arthritic pain (e.g., pain associated with crystalline arthritis, osteoarthritis, psoriatic tis, gouty arthritis, reactive arthritis, rheumatoid arthritis or Reiter's arthritis), lumbosacral pain, musculo— skeletal pain, headache, migraine, muscle ache, lower back pain, neck pain, toothache, dental/maxillofacial pain, visceral pain and the like. One or more of the painful conditions contemplated herein can comprise mixtures of various types of pain provided above and herein (e.g. nociceptive pain, atory pain, neuropathic pain, etc.). In some embodiments, a ular pain can dominate. In other embodiments, the painful condition comprises two or more types of pains without one dominating. A skilled clinician can ine the dosage to achieve a therapeutically effective amount for a particular t based on the painful condition.

In certain embodiments, the painful condition is inflammatory pain. In certain embodiments, the painful condition (e.g., inflammatory pain) is associated with an inflammatory disorder and/or an autoimmune disorder.

In certain embodiments, the condition is a liver disease and, in n ments, the composition further includes an agent useful in treating liver disease.

Exemplary liver diseases include, but are not limited to, drug—induced liver injury (e.g., inophen—induced liver injury), hepatitis (e.g. , chronic hepatitis, viral hepatitis, alcohol—induced hepatitis, autoimmune hepatitis, steatohepatitis), non—alcoholic fatty liver disease, alcohol—induced liver disease (e.g., alcoholic fatty liver, alcoholic hepatitis, alcohol— related cirrhosis), hypercholesterolemia (e.g., severe hypercholesterolemia), hyretin— related tary amyloidosis, liver sis, liver cancer, primary y cirrhosis, cholestatis, cystic e of the liver, and primary sclerosing cholangitis. In certain embodiments the liver disease is associated with inflammation.

In certain embodiments, the condition is a familial amyloid neuropathy and, in certain ments, the composition further includes an agent useful in a familial amyloid neuropathy.

A “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, cent) or adult subject (e.g., young adult, middle—aged adult or senior adult)) and/or other non—human animals, for example mammals [e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); and commercially relevant mammals such as mice, rats, hampsters, cattle, pigs, horses, sheep, goats, cats, and/or dogs] and birds (e.g., commercially nt birds such as chickens, ducks, geese, and/or turkeys). In certain embodiments, the t is a non— human animal. The non—human animal may be a male or female and at any stage of development. A non—human animal may be a transgenic animal.

As used herein, and unless otherwise specified, the terms “treat,77 4‘treating” and “treatment” plate an action that occurs while a subject is suffering from the specified disease, disorder or condition, which reduces the severity of the disease, disorder or condition, or retards or slows the ssion of the disease, disorder or condition (“therapeutic treatment”), and also plates an action that occurs before a subject begins to suffer from the specified disease, disorder or condition hylactic treatment”).

In general, the “effective amount” of an active ingredient refers to an amount sufficient to elicit the desired biological response. As will be appreciated by those of ordinary skill in this art, the effective amount of a nd of the invention may vary ing on such factors as the desired biological endpoint, the pharmacokinetics of the active ingredient, the disease being treated, the mode of administration, and the age, health, and condition of the subject. An effective amount encompasses therapeutic and prophylactic treatment.

As used herein, and unless ise specified, a “therapeutically effective amount” of an active ingredient is an amount sufficient to provide a therapeutic benefit in the treatment of a disease, disorder or condition, or to delay or minimize one or more symptoms associated with the disease, disorder or condition. A therapeutically effective amount of an active ingredient means an amount of the active ient, alone or in combination with WO 63468 other agents or therapies, which es a therapeutic benefit in the treatment of the disease, er or condition. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of disease or condition, or enhances the therapeutic efficacy of another therapeutic agent.

] As used herein, and unless otherwise specified, a “prophylactically effective amount” of an active ingredient is an amount sufficient to prevent a disease, disorder or condition, or one or more symptoms associated with the e, disorder or condition, or prevent its recurrence. A prophylactically effective amount of an active ingredient means an amount of the active ingredient, alone or in ation with other agents or therapies, which es a prophylactic benefit in the prevention of the disease, disorder or condition. The term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or es the prophylactic efficacy of another prophylactic agent.

] The active ingredient may be administered in such amounts, time, and route deemed necessary in order to e the desired result. The exact amount of the active ingredient will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular active ient, its mode of administration, its mode of activity, and the like. The active ingredient, whether the APPL itself, or the APPL in combination with an agent, is preferably formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the active ingredient will be decided by the ing physician within the scope of sound medical nt. The specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the er being treated and the severity of the disorder; the activity of the active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific active ient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.

The active ingredient may be administered by any route. In some embodiments, the active ingredient is administered via a variety of routes, ing oral, intravenous, intramuscular, intra—arterial, edullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, enteral, sublingual; by intratracheal instillation, ial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol. In general the most appropriate route of administration will depend upon a variety of factors ing the nature of the active ingredient (e.g., its stability in the environment of the gastrointestinal tract), the condition of the subject (e.g., whether the subject is able to tolerate oral administration), etc.

The exact amount of an active ingredient required to e a eutically or prophylactically effective amount will vary from subject to subject, depending on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like. The amount to be stered to, for example, a child or an adolescent can be ined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.

Examples In order that the invention described herein may be more fully understood, the following examples are set forth. It should be tood that these es are for illustrative purposes only and are not to be construed as limiting this invention in any manner.

Amino acid-, e-, and ptide-lipids (APPL) for drug delivery To address the challenges associated with delivery efficiency, specificity, and toxicity of biological agents, we developed a potent and selective siRNA delivery system with a broad therapeutic window through rational design and optimization of novel amino acid—based lipid derivatives.

Previously, our group has pursued a combinatorial synthetic ch to develop new cationic lipids (lipidoids) for siRNA delivery. See, e. g., Akinc, A., et al., A combinatorial y of lipid-like materials for delivery ofRNAi therapeutics. Nat Biotechnol, 2008. 26(5): p. 561—9; Love Kevin, T., et al., like materials for low-dose, in vivo gene silencing. Proc Natl Acad Sci U S A. 107(5): p. 1864—9; Siegwart, D.J., et al., Combinatorial synthesis of chemically e core-shell nanoparticles for intracellular delivery. Proc Natl Acad Sci U S A. 108(32): p. 12996—3001. A number of these compounds have shown significant silencing effects in vivo. See, e.g., Leuschner, F., et al., Therapeutic siRNA silencing in inflammatory monocytes in mice. Nat Biotechnol. 29(l l): p. 1005—10.

Prior studies have identified key chemical and structural features and formulation methods for the development of new materials. See, e. g., Akinc, A., et al., Development of lipidoid- siRNA formulations for systemic delivery to the liver. Mol Ther, 2009. 17(5): p. 872—9; Akinc, A., et al., Targeted delivery ofRNAi therapeutics with endogenous and exogenous ligand- based mechanisms. Mol Ther. 18(7): p. 1357—64; Semple, SC, et al., Rational design of cationic lipids for siRNA delivery. Nat Biotechnol. 28(2): p. 172—6. For example, active nds possess 12 or more carbons in tail length and multiple tails. See, e. g., Love Kevin, T., et al., Lipid-like materials for low-dose, in vivo gene silencing. Proc Natl Acad Sci U S A. 107(5): p. 1864—9. In order to improve cy, tissue and cell—type selectivity, and tolerability, new chemical scaffolds need to be designed and investigated.

Amino acids are natural ng blocks of peptides and proteins in nature.

Amino acid derivatives can be metabolized by the human body; therefore, these materials are likely well tolerated and safe as therapeutics. Additionally, es play significant roles in ne transport, endogenous cellular signaling and trafficking pathways, and offer tremendous potential in leveraging such interactions to enhance the delivery efficiency of systems which incorporate peptide es. Because of their significant physiological functions and safety in humans, amino acid—based materials, such as insulin and trastuzumab, have been widely d as ments and eutic medicines in the clinic for e es. Studies have shown that it is feasible to apply amino acid—derivatives for gene delivery or siRNA ry. See, e. g., Prata, C.A., et al., Lipopliilic peptides for gene delivery. Bioconjug Chem, 2008. 19(2): p. 418—20; Adami, R.C., et al., An amino acid-based amplioteric liposomal delivery systemfor systemic administration of siRNA. Mol Ther. 19(6): p. ll4l—Sl; Margus, H., K. Padari, and M. Pooga, Cell-penetrating peptides as versatile vehicles for oligonucleotide ry. Mol Ther. 20(3): p. 525—33. Combining the advantages of both natural properties of amino acids and ural features of lipidoids, we d a strategy of structural optimization through an iterative screening process and rationally designed a series of amino acid—based lipid derivatives. We report the design, synthesis, and biological evaluation of this new series of amino acid—based lipid derivatives. This efficient and rational strategy yielded a lead material cKK—El2. We systematically investigated its delivery efficiency, tissue and cell—type selectivity, tolerability, and mechanism of action.

Current results demonstrate that this delivery system is a novel platform for efficient, selective, and safe ry of siRNA, which shows great potential for the treatment of various diseases.

General Methods Method 1. ation of Compounds of Formula (I)-(III). Conjugation to formula (i).

A mixture of amino acids, peptides or polypeptides and the conjugating reagent (an epoxide, thiirane, or aziridine) (a ratio of 1.5:1 to 3:1 conjugating reagent to amine) in EtOH was irradiated in the microwave oven at 150 0C for 5 h. The reaction e was purified by flash column tography. If amino acids, es or polypeptides were in salt form, triethylamine was added to the solution and stirred for 30 minutes at room temperature before irradiation.

SchemeA. o o o R1 R1 Y 150°C Y ORA4 HZN A4+ A —> + OR RL EtOH HY/TA/N\)\ / YH RL HYAVN\r\ R1 RL RL Y O,S,NRY SchemeB.

R1 o YH NH HZNJ\H/H 150 °c RKHL N ORA4+ AR L N EtOH RL\/ fiR'] O R 1 Y=o,s,NRY Scheme C.

R1 o H + —> L N HzN ORA4 ‘/ RL EtOH NH2 HY\/\J Scheme D.

RL\J NH2 r /\ N HY RL/\/ 0 o YH NH H Y 150 °c + —> J\/N H2N ORA4 RL RL EtOH 0 o HY Y = o, s, NRY \ NH2 HY\/\J Scheme E.

L R'- HY\/\/\ /\/¢YH NH2 N o o H Y R 150 °c + K H é A4 H2N ORA4 0R RL EtOH HY j‘ o \ o n ” \/ Y = o s, NRY RL HY/\/N RL \l—KRL Method 2. Preparation of Compounds of Formula (I)-(III). Conjugation to formula (ii).

A mixture of amino acids, es or polypeptides and conjugating reagent (acrylate or acrylamide) (a ratio of 1.5:1 to 3:1 acrylates or conjugating reagent to amine) in ethanol (EtOH), isopropanol (iPrOH), or acetonitrile was heated to 90 0C and stirred for 2 hours to 2 days. The on solution was concentrated with silica gel and ed with flash column chromatography.

Scheme F. o o R1 R1 0 ORA4 ORA4 WNW/1k + X‘ & ORA4 W/ R HN\/\n/x x N X EtOH \RL RL’ \n/\/ \/\n/ \RL R1 0 o o o Scheme G. o R1 0 \X/“\/\HNNVkORA‘; R1 O 0 R 1 H + X 90°C NVKORM /\n/ \ RL —> O 1 EtOH R O HZN H 0 RL\ N o R1 x N ORA4 X=o,s,NRX o R1 Scheme H.

R1 O H + X & o H2N 0RA4 N \ RL EtOH /\/N o 0 RL 0 O x’ x=o,s,NRX \x 0 Scheme 1.

NH2 0 X‘RL x N x o RL’ W o H + /\n/ \RLLC> H2N A4 0 OR EtOH 0 NH O x=o,s,NRX ,x N o o X,RL \x o Scheme]. 0 O L /U\/\ /\/u\ RL NH2 R\X N x’ O X O H H N \ L—>90°C N HZN ORA4 + / O N ORA4 EtOH O L o n R\XJJ\) o n NH2 RL’X\”/\/N O 0 Method 3. Preparation of Compounds of Formula (I)-(III). Conjugation to formula (iii).

To a solution of amino acids, peptides or polypeptides and ating reagent (aldehyde) (a ratio of 1.5:1 to 3:1 aldehydes to amine) in THF was added sodium triacetoxyborohydride (NaBH(OAc)3) at rt. The reaction mixture was stirred for 3 d at rt. The reaction solution was concentrated with silica gel and ed with flash column tography.

Scheme K.

O O O R1 R1 0 NaHB(OAc)3 $0M“ ORA4 HZN A4+ JL OR THFt,r HN RL RL N RL H RL \/ \/ v Scheme L.

R1 o RLAN ORA4 R1 O H H 0 NaHB(OAc)3 O R1 + —> H2N ORA4 R1 H RL THF,rt o O R1 A H RL N ORA4 RL/i o R1 Scheme M.

R1 o H 0 NaHB(OAc)3 RK/N H2N ORA4 HJLRL THF, rt 0 RL Scheme N.

NH2 rRL RL\/N O O O H NaHB(OAc)3 + JL NH H2N ORA4 H RL THF, rt RL\/N NH2 j] Scheme 0. o NaHB(OAc)3 RL 0 H + JL L THF,rt H H2N ORA4 H R N ORA4 O n RLJ O n R\/NWL NH2 Method 4. Preparation of Compounds of Formula (IV) Compounds of Formula (IV) may be prepared via sation of a 1,2— diamine with an activated oxalic acid, wherein X1 is a leaving group, e.g., bromo, chloro, or iodo, to provide the cyclized product. Groups of a (i), (ii), or (iii), may be installed after cyclization, e.g., for example, via addition to an amino side chain substituent of R1, or to imino nitrogen groups RQ. Other groups on the ld, 6.57., R2 groups, may be installed prior to cyclization. For e, R2 may be a group of the formula (i), (ii), or (iii) installed prior to cyclization.

Scheme P.

R1 R2 NH1:12:03 2HX1 12: 1,2-diamine oxalicacid (IV) derivative Method 5. Preparation of Compounds of Formula (V) Compounds of Formula (V), and (VI) may be ed via condensation of a l,l—diamine with an activated malonic acid, wherein X1 is a leaving group, e.g., bromo, chloro, or iodo, to provide the cyclized product. Groups of formula (i), (ii), or (iii), may be installed after cyclization, e.g., for example, via addition to an amino side chain substituent of R1, or to imino nitrogen groups RQ. Other groups on the ld, 6.57., R2 groups, may be installed prior to cyclization. For example, R2 may be a group of the formula (i), (ii), or (iii) installed prior to cyclization.

Scheme Q.

R2 Q ‘NH x1 R1—< + R1—<N [NH X1 l R2 Q 2HX1 1,1-diamine l derivative Method 6. Preparation of Compounds of a (V1) Compounds of Formula (VI) may be prepared via condensation of a hydrazine with an activated succinic acid, wherein X1 is a leaving group, e.g., bromo, chloro, or iodo, to provide the cyclized product. Groups of formula (i), (ii), or (iii), may be installed after cyclization, e.g., for e, via addition to an amino side chain substituent of R1, or to imino nitrogen groups RQ. Other groups on the scaffold, 6.57., R2 groups, may be installed 2012/062222 prior to cyclization. For example, R2 may be a group of the formula (i), (ii), or (iii) installed prior to cyclization.

Scheme R.

Q R: Q Ri X1 /N NH R1 R2_ R1 RZ—NH ; Q R1 2 HX1 Q R1 hydrazine succinic acid (VI) derivative derivative Exemplary Precursors Table 1. Amino Acids and Esters Name, Symbol Amino acid side chain (R )* Amino acid or ester N N/ H2N H ORA4 Arginine R ’ m j]: NH N NH2 N NH2 VB] 0 :/N’R6 6’N\// HZN N\ ORA4 H1st1d1ne. . . R H ’ N“ N“ NH N N§/ HN\// ORA4 Lysine K R7’N‘R6 NH2 ’ NH2 2012/062222 Table 1. Amino Acids and Esters Name, Symbol Amino acid side chain (R )* Amino acid or ester H2N{3:0 ORA4 Aspartic Acid D Glutamic Acid E R50 0 HO 0 WeORA4 IO 0 Serine ORA4 0R6, OH #0 Threonine T ORA4 0R6, OH Wm o Asparagine N R7’N‘R6 NH2 {3:0ORA4 ORA4 Glutamine Q 0 N’ 0W0NH2 Cysteine C #0ORA4 Glycine G H2N\/U\ORA4 Table 1. Amino Acids and Esters Name, Symbol Amino acid side chain (R )* Amino acid or ester Proline P O/lk‘g O/lk’g ZI O503: exemplary RI-R3 cyclized group Alanine A —CH3 NIZ‘§:O ORA4 Beta—alanine —H, H /\/u\ HZN 02“ H N2 ILORA“ Valine V —CH(CH3)2 . H2N Isoleucme I —CH(CH3)(CH2CH3) ORA4 INZof; O50)>A e L —CH2CH(CH3)2 E f3:ORA4 Methionine M IN263:0 0RA4 Phenylalanine F Table 1. Amino Acids and Esters Name, Symbol Amino acid side chain (R )* Amino acid or ester 0R5, ne Y 2 ’a Tryptophan W / / N HN * R6 and R7 are en in the precursor, and, upon conjugation, are independently selected from the group consisting of hydrogen, ally substituted alkyl, optionally tuted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or a group of formula (i), (ii), or (iii).

Table 2. Peptides and Polypeptides Name, Symbol Amino acid N H 2 linear lysine—lysine linear K—K H2N OH Table 2. Peptides and Polypeptides Name, Symbol Amino acid H N2 . . . . HN cychc lysme—lysme cychc K—K H2N ORA4 K-K-K polylysine n = 2 K—K—K—K As above; n = 3 K—K—K—K—K As above; n = 4 polysine —K As above; n = 3—12 (500—2000 g/mol) PK—SOO polysine —K As above; n = 6—33 (1000—5000 g/mol) PK-1000 polysine K—(K)n—K As above; n 2 26—102 (4000—15000 g/mol) PK4000 polysine K—(K)n—K As above; n = 102—204 (15000—30000 g/mol) PK—15000 polysine K—(K)n—K As above; n = 204-480 (30000—70000 g/mol) PK—30000 Table 2. Peptides and Polypeptides Name, Symbol Amino acid HNYNH2 linear arginine—arginine linear R—R cyclic arginine—arginine cyclic R—R ginine R-(R)n-R (5000—15000) PR-5000 linear histidine—histidine linear H—H cyclic histidine—histidine cyclic H—H Table 2. es and Polypeptides Name, Symbol Amino acid polyhistidine H-(H)n-H H2N ORA4 (5000-25000) PH-5000 o n n=32—l6l linear glycine—glycine linear G—G H2N/\n/N\/U\OH cyclic glycine—glycine cyclic G—G H¢ HzNJY O linear arginine—lysine linear AK HzN/[n/ 0 linear cysteine—lysine linear CK O COZH HzN/[n/ O linear aspartic acid—lysine linear DK 0 Table 2. Peptides and Polypeptides Name, Symbol Amino acid COZH llnear lc ac1d—lys1ne. . . . llnear EK. HzN/fif H N/En/N2 OH linear phenylalanine— linear PK 0 lysine N H2 H2N/\n/N OH linear glycine—lysine linear GK N H2 HzNjir O linear isoleucine—lysine linear 1K N H2 H2N¢ O linear leucine—lysine linear LK 2012/062222 Table 2. Peptides and Polypeptides Name, Symbol Amino acid ZIf3“ IN20:2—\' 0I linear methionine—lysine linear MK linear proline—lysine linear PK CONH2 H2N OH linear glutamine—lysine linear QK H2Nj\n/ O linear serine—lysine linear SK O Table 2. Peptides and Polypeptides Name, Symbol Amino acid linear tryptophan—lysine linear WK N H2N OH linear ne—lysine linear YK H2N OH linear lysine—threonine linear KT 0 H2N OH linear lysine—valine linear KV 0 H2N OH Table 3. Conjugating reagents Table 3. atin rea_ents Name Structure E11 WW E13 W E14 W E15 W E16 W A11 W A13 W 010 / 011 \jiOA/W 012 $0 013 \jLO 014 V10 N10 VLN/WVW N11 VLNWA/ N12 VLN N13 VL Table 3. Con'u__atin rea_ents Name Structure Synthetic Procedures Example 1. Synthesis of APPLs s A—R show the general synthetic routes to APPLs of Formula (I) to (VI), of the present invention. Application of these methods generated a y of APPLs, depicted in Tables 4 and 5.

Compounds were named by combination of the abbreviation of amino acids, aldehydes (A), acrylates (O), amides (N), or epoxides (E), and the length of carbon chains.

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Compd Chemical formula Calcd. Observed Tail # A—E12 C27H54NO3+ 440.4098 440.4336 2 C—E12 NO3S+ 472.3819 472.4303 2 D—E12 C28H54NO5+ 484.3997 484.4327 2 E—E12 NO5+ 53 17 2 I—E12 C30H60NO3+ 482.4568 482.4461 2 K—E12 C42H85N204+ 681.6504 681.6009 3 L—E12 C30H60NO3+ 482.4568 482.4771 2 M—E12 C29H58NO3S+ 500.4132 500.4471 2 N—E12 C40H79N205+ 667 .5984 667.5894 3 P—E12 C17H32NO2+ 282.2428 282.2585 1 Q—E12 C29H57N204+ 497.4313 497.4268 2 R—E12 C54H109N405+ 893.8392 893.8400 4 cKG—E12 C32H64N304+ 554.4891 554.4852 2 cKT—E12 C34H68N305+ 598.5153 598.5179 2 cYK—E12 N305+ 660.5310 660.5350 2 cLK—E12 C36H72N304+ 610.5517 610.5556 2 2* C36H70N306+ 640.5259 16 2 cMK—E12 C35H70N304S+ 628.5082 628.5072 2 2 C35H70N304+ 596.5361 596.5330 2 cAK—E12 C33H66N304+ 568.5048 568.4992 2 cEK—E12 C35H68N306+ 626.5103 626.5053 2 cIK—E12 N304+ 610.5517 610.5501 2 cSK—E12 C33H66N305+ 584.4997 29 2 cKK—E10 C52H105N406+ 881.8029 881.8042 4 cKK—E12 C60H121N406+ 993.9281 993.9224 4 cKK—E14 C68H137N406+ 1106.0533 1106.0709 4 cKK—E16 C76H153N406+ 1218.1785 1218.2002 4 Table 5.

Compd Chemical formula Calcd. Observed Tail # A—A12 C27H56NO2+ 426.4306 426.4244 2 C—A12 C27H56NO2S+ 26 458.3857 2 D—A12 C28H56NO4+ 470.4204 470.4188 2 E—A12 C29H58NO4+ 484.4360 484.4319 2 I—A12 C30H62NO2+ 75 468.4714 2 K—A12 C54H111N202+ 819.8640 819.8657 4 L—A12 C30H62NO2+ 468.4775 468.4752 2 M—A12 C29H60NO2S+ 486.4339 486.4318 2 N—A12 C28H57N203+ 469.4364 28 2 P—A12 C17H34NO2+ 284.2584 284.2512 1 Q—A12 C29H59N203+ 20 483.4543 2 R—A12 C42H87N402+ 679.6824 679.6783 3 KK—A12 C84H171N403+ 1284.3346 1284.3458 6 KKK—A12 C114H231N604+ 1748.8051 1748.8340 8 cKK—A12 C60H121N402+ 929.9484 929.9445 4 A—O12 NO4+ 330.2639 330.2582 1 C—012 C33H64NO6S+ 602.4449 602.4426 2 D—012 C19H36NO6+ 374.2537 374.2492 1 E—012 C20H38NO6+ 388.2694 388.2672 1 F—O12 NO4+ 406.2952 406.2896 1 H—012 N306+ 636.4946 636.4969 2 K—O12 C66H127N2010+ 1107.9485 1107.9417 4 M—O12 C20H40NO4S+ 390.2673 390.2628 1 N—012 C19H37N205+ 373.2697 68 1 P—012 C20H38NO4+ 356.2795 79 1 Q—012 C20H39N205+ 387 .2853 387.2831 1 R—O12 C21H43N404+ 415.3279 415.3235 1 S—012 C18H36NO5+ 346.2588 346.2521 1 T—012 C19H38NO5+ 360.2744 360.2733 1 Chemical formula Observed V—012 C20H40NO4+ 358.2952 358.2905 W—Ol2 C26H41N204+ 445.3061 445.3010 * formation of ethyl ester. Compounds derived from poly—L—lysine are not included.

Exemplary compounds of Table 5: OH OH 1/g ’g C10Hz1/g M% W101I:M1:3” A-E12 C-E12 D-E12 OH OH OH C10H21I$C1OH21/$ OH OH C10"‘21/g C10H21 C10Hz1 E-E12 C1on1 F-E12 (3-E12 C10Hz1 N C10"‘21’g C1on1 OH / C10"‘21 N§/ V010H21 H-E12 HO I-E12 9 9 1/g C10H21 C10H21/</N CH C1on1 L-E12 M-E12 P-E12 R-E12 WO 63468 C10H21’g O OH OH C10H21/g O N K-E12 C10H21 HO OH C10H21KKOH Y-E12 C10H21 O OHO m MNH HN HN O HOD/C1OH21 O HO C10H21 N Nj/ C10H21 C10H21 cKG-E12 cKT-E12 OH OH O O HN NNHHN O HOD/C10H21 O HOj/C10H21 N N C10H21 C10H21 cYK-E12 cLK-E12 OH OH O O HONNH 8 / MNH O HN HN O HOj/C1oH21 O HOj/C10H21 N N C10H21 C10H21 cDK-E12 cMK-E12 OH OH O O NH YLNH HN HN O HOj/C1oH21 O HOD/C10H21 N N C10H21 C10H21 2 cAK-E12 OH OH SH 0 H2N o KHkNH NH HN HN O HOD/CmHm O HOD/C1OH21 N N C10"‘21 C10H21 cCK-E12 CQK-E12 OH OH O O O HOD/C10H21HOj/C10H21 N N C10Hz1 C10Hz1 cPK-E12 cFK-E12 OH OH O HOWNH 10H21j/C10H21Nj/ CWK-E12 YC10H21S/C10H21CEK-E12 OH OH O Flo/\HOkNI—I Wmoj/C1OH21Nj/ HNfiLOj/C10H21Nj/ C1on1 clK-E12 YC10H21 CSK-E12 OH OH C11 H C11"‘23 23W O C11H23 W 0 7 N OH ( O“ l/N c11 H23 C11"‘23 SH C11st A-A12 C-A12 D-A12 OH 2012/062222 C11H23W C11H23W CMHZBfi O C11Hz3 C11H23 OH E'A12 C11"‘23 F-A12 G-A12 C11H23 N N C11Hz3 / C11 H23 C11"‘23 H-A12 I-A12 L-A12 C H C11 H 11 23W 0 23w 0 N N C1 1 H23 r r \\ O OH OH C11"‘23 C11Hz3 N 8\ NH2 M-A12 N-A12 P-A12 O NH2 Q-A12 R-A12 C11H23W O C11H23W O C11H23W O N N N 1/ OH I/ OH 1/ OH C11 H23 C11 H23 C11 H23 OH OH S-A12 T-A12 V-A12 ( OH rN OH NH C11H23 W-A12 OH Y_A12 C11H23 W O (312st N t (I) O OH O O C11H23 K-A12 N HN OH C11H23VNW SH C11H23 A-012 C12H25/ C-012 C12Hz5 (I) O ([312H25 $12H25 O O O O ('312H25 O O O O OH HN “N O OH OH O HN\)J\ OH E-012 D-012 HO 0 F-O12 G-O12 '12 25 C12H25 C12HZS O O I l O O O O O O OH HN HN OH OH /O N§/ 012st H-O12 l-O12 L-O12 $12H25 $12H25 O O O 0 C12st (‘3 o O O HN HN OH OH 0 GAO“ S NH2 M-O12 N-012 P-012 ('312H25 O O 3312st O O C H N N/Qk / 12 25 H H 0 NH2 0-012 R-O12 €312st 25 $312st 0 O O O O O O O O HN HN HN OH OH OH OH OH 3-012 T-O12 V-012 ([312st $312st 0 o o o OH HN w-o12 0H Y-O12 ’ ,and O O C312H25/ O N C12H25/ OH K-O12 O N O o \C12H25 Example 2. Alternative synthesis of compound 23 (cKK-E12) BocHN-CHC-O 0 (EH CszN . 1. TFA, rt NH Pol/Q H2 9H2 —’ HN —> CH2 2. pyridine, rt ACOH/CHZCIZ (:ZHZ 0 NHCbz NHCbz A B C10H21 O o VAN HO NH HZN HO NH 2AcOH TEA. EtOH HN C1oH21 HN C H /—< MW 10 21 O N OH O 1 HO C10H21 c 23 (cKK-E12) Synthesis of nd B. Compound A (487 mg, 1.02 mmol) was charged in a ml flask and trifluoroacetic acid (TFA, 1.3 mL) was added dropwise at 0 0C. The reaction mixture was warmed to room temperature and stirred for 30 min. The ts were evaporated under reduced pressure and the TFA salts in DMF (3.5 mL) were added dropwise to pyridine (100 mL) at 0 0C. The reaction mixture was slowly warmed to room temperature and stirred for overnight. The solvents were evaporated under reduced re and the white solid was washed with EtOAc to give pure B in 69% yield. MS: m/z 525 (M+H+); 1H NMR (500 MHZ, DMSO, ppm): 5 1.29-1.40 (m, 8H, CHZCHZ), 1.61-1.68 (m, 4H, CH2), 2.97 (dd, J = 6.0, 12.5 Hz, 4H, NCHZ), 3.79 (br, 2H, COCH), 7.22 (t, J: 5.5 Hz, 2H, aromatic), 7.33- 7.37 (m, 8H, aromatic), 8.10 (s, 2H, NH).

WO 63468 Synthesis of compound C. A cloudy solution of compound B (95 mg, 0.18 mmol) in 50% acetic acid/CHZClZ (6 mL) was added Pd on charcoal (10 wt %, 36.5 mg). The black suspension was ed for 5 mins and hydrogen gas introduced. The reaction mixture stirred at rt ght and was then filtered through a layer of , which was washed several times with MeOH. The combined filtrates were concentrated to obtain a yellow viscous oil, which was solidified by adding EtOAc. The solid was washed by ethyl acetate to yield compound C in 90% yield. MS: m/z 257 (M+H+); 1H NMR (500 MHz, D20, ppm): 5 1.39-1.52 (m, 4H, CH2), 1.67-1.71 (m, 4H, CH2), 1.84-1.88 (m, 4H, CH2), 2.99 (t, J: 7.5 Hz, 4H, NCHZ), 4.14 (t, J: 5.0 Hz, 2H, COCH).

Synthesis 0fcomp0und 23 (cKK-EIZ). A mixture of compound C (169.2 mg, 0.45 mmol) and 1,2—epoxydodecane (523 mg, 2.7 mmol) in EtOH was added triethylamine (182 mg, 1.8 mmol), which was stirred 30 mins at rt. The reaction mixture was then irradiated in the microwave oven at 150 0C for 5 h. The mixture was purified by flash column chromatography to obtain compound 23 (in 52% yield) as a light yellow oil. MS: m/z 993 (M+H+); 1H NMR (500 MHz, DMSO, ppm): 8 0.87 (t, J = 7.0 Hz, 12H, CH3), 1.21-1.39 (m, 80H, CH2), 1.64-1.67 (m, 4H, CH2), 2.25-2.44 (m, 12H, NCHZ), 3.44 (br, 4H, CHOH), 3.79 (br, 2H, COCH), 4.21 (d, J: 3.0 Hz, 2H, CHOH), 4.27 (d, J: 3.0 Hz, 2H, CHOH), 8.11 (br, 2H, CONH).

Example 3. Synthesis of Compound D It is envisioned compound D can be synthesized by reaction of 23 with Lawesson’ s reagent in dry toluene. 23 D Example 4. Synthesis of nd E It is envisioned compound E can be synthesized by reaction of 23 with ylamine hloride or other substituted amines in methanol. 23 E Biolo ical Methods siRNA Formulations Formulation A APPL, distearoyl phosphatidylcholine (DSPC), cholesterol and mPEG2000— DMG were solubilized in 90% ethanol at a molar ratio of 50:10:38.5:l.5. The siRNA (against firefly luciferase or fVII) was solubilized in 10 mM citrate, pH 3 buffer at a tration of 0.4 mg/mL. The ethanolic lipid solution and the aqueous siRNA solution were pumped by means of a syringe pump through a microfluidic mixing chamber to spontaneously form siRNA—containing lipid nanoparticles. Lipids were combined with siRNA at a total lipid to siRNA ratio of 7:1 (wt:wt). These ations were dialyzed against PBS to remove ethanol and exchange buffer. ation B APPLs were ated with cholesterol (Sigma—Aldrich), DSPC (1,2— royl—sn—glycero—3—phosphocholine, Avanti), mPEG2000—DMG esized by Alnylam), and siRNA via a microfluidic based mixing device See, e. 57., Chen, D., et al., Rapid Discovery ofPotent siRNA-Containing Lipid Nanoparticles Enabled by Controlled Microflnidic Formnlation. J Am Chem Soc. Formulations were then dialyzed against PBS in 3,500 MWCO dialysis cassettes (Pierce) overnight. Particles were characterized with a modified Ribogreen assay (Invitrogen) for siRNA entrapment and dynamic light scattering (ZetaPALS, aven Instruments) for mean particle diameter. cKK—E12 formulations were made from cholesterol, DSPC, and mPEG2000—DMG using a similar method at a molar ratio of 50:10:38.5:l.5. This formulation afforded a particle diameter of 60—70 nm with approximately 65% siRNA entrapment.

In Vitro Luciferase Gene Silencing HeLa cells, stably expressing firefly luciferase and Renilla luciferase, were seeded (14,000 cells/well) into each well of an opaque white 96—well plate(Coming—Costar) and allowed to attach overnight in growth medium. Growth medium was composed of 90% phenol red—free DMEM, 10% FBS, 100 units/ml penicillin, 100 mg/ml streptomycin (Invitrogen). Cells were ected with LNPs formulated with anti—luciferase siRNA by addition of formulated particles to growth medium. Transfections were performed in quadruplicate. Cells were allowed to grow for 1 d at 37°C, 5% CO2 and were then analyzed for luciferase expression. Control experiments were performed with Lipofectamine 2000, as described by the vendor (Invitrogen). Firefly and Renilla rase expression was ed using Dual—Glo assay kits (Promega). Luminescence was measured using a Victor3 luminometer (Perkin Elmer).

In Vivo Factor VII Gene Silencing in Mice C57BL/6 mice (Charles River Labs) were used for siRNA silencing experiments. Prior to injection, ations were diluted in PBS at siRNA concentrations (SEQ ID NO 1 (siFVII sense): 5’—GGAucAucucAAGucuuAcTi‘T—3’; SEQ ID NO 2 (antisense): 5’(EuA;»\(‘n»\cuuGAGAuGAuccTi‘Tl}’) such that each mouse was administered a dose of 0.01 mI/g body—weight. Formulations were administered intravenously via tail vein injection. After 48 or 72 h, body—weight gain/loss was measured and mice were hetized by isofluorane tion for blood sample collection by retroorbital eye bleed. Serum was isolated with serum tion tubes (Falcon tubes, Becton Dickinson) and Factor VII protein levels were analyzed by chromogenic assay (Biophen FVII, Aniara Corporation). A standard curve was constructed using samples from PBS—injected mice and relative Factor VII expression was determined by comparing treated groups to untreated PBS control.

Biodistribution Cy5.5-labled siRNA-cKK-E12 formulation in mice.

The mice mentioned above were ically injected with ated Cy5.5— labeled siRNA at a dose of 1 mg/kg of total siRNA. The mice were sacrificed 1 hour or 24 hours post injection; the pancreas, spleen, liver, kidneys, ovaries, uterus, heart, lungs, and thymus as well as a section of the adipose tissue and muscle tissue were then removed and . The organs were ed with an Ivis imaging system from r using an excitation wavelength of 675nm and an emission wavelength of 720nm. The data were WO 63468 processed using the Living Image software from Caliper. Signal strength of the individual organs was normalized against the total signal strength of all organs.

In Vitro siRNA Transfection Assay and Microscopy.

Effects of apolipoproteins were evaluated through an in: vitro siRNA transfeetitm assay in l’lelsa cells as previously reported. l’lelia cells, stably expressing firetl y lueiferase and Renllla lueiferase were seeded in an opaque white 96—well plate (Corning— Costar) overnight. Cells were transfeeted by eKK—El2 formulated with 50 ng of firefly— speeifle siluc in quadruplicate. Apolipeproteins (lilitzgeraltl industries) were incubated with cKK~El2 formulations for 5 mins befere adding to cells. After 24 h incubation at 37 0C, 5% C02, eells were ed for lueiferase expression using Dual—file assay kits (Prernega). For visualizatien of cell uptake, eKK-E. 32 was ated with an Alexa-E'luer {i47mlabeled siRNA and incubated with Belt: eells fer 3 l1. Cells were then fixed in 4% paraformaldehyde, permeabilized with 0.1% saponin and stained with t. All images were acquired using an Opera spinning disc confocal system (Perkin Elmer), and the data was analyzed using Acapella Software (Perkin .

Discussion Single amino acids were d with aldehydes, acrylates, and es to produce APPLs. The newly—synthesized single amino acid—based lipid derivatives were ted for their capacity to silence hepatic genes in mice. A validated c target, Factor VII (a blood clotting factor), was selected as a ing marker. See, e. g., Akinc, A., et al., A combinatorial library of lipid-like materials for delivery ofRNAi therapeutics. Nat Biotechnol, 2008. 26(5): p. 561—9. New lipid derivatives were formulated with cholesterol, DSPC, PEG—lipid, and siRNA via a microfluidic based mixing technology. See, e. 57., Chen, D., et al., Rapid Discovery ofPotent siRNA-Containing Lipid Nanoparticles Enabled by Controlled Microflaidic Formalation. J Am Chem Soc. Formulations that were le in solution or had no siRNA entrapment were not screened. Stable formulations were injected in mice through systemic administration at a dose of 1 mg/kg (Figure 1). From this initial screening, we fied that K—El2 was more potent than others. The hit rate (over 50% silencing) was one out of 60 compounds (i.e. 1.7%, including those compounds not ed due to le instability or no entrapment of siRNA).

The enhanced potency of K—El2 led to our design of a second set of lysine— based peptide and polypeptide—lipid derivatives. Lysine—based dipeptides were reacted with epoxides to give diketopiperizine APPLs. Microwave irradiation was utilized to produce these lds, which dramatically reduced the on time from 3 days to 5 hours. In addition, to further confirm the chemical structure and improve chemical availability for large—scale synthesis, an alternative synthetic route was ped for the synthesis of cKK- E12 (Example 2). Diamine 5 was synthesized according to the method reported previously (Bergeron, R.J., et al., Macromolecular Self-Assembly ofDiketopiperazine Tetrapeptides. J.

Am. Chem. Soc., 1994. 116(19): p. 8479—84; Kaur, N., et al., A ation of Diketopiperazine Self-Assembly Processes: Understanding the Molecular Events Involved in N—(Fumaroyl)diketopiperazine ofL-Lys (FDKP) Interactions. Mol. Pharmaceutics, 2008. (2): p. 294—315), which reacted with 1,2—epoxydodecane to afford cKK-E12. Compound (C) underwent reductive amination or Michael addition reactions with dodecanal or dodecyl acrylate to yield cKK-A12 and cKK-012. ons between lysine—lysine and poly—L—lysine (molecular weight from 500—70000 g/mol) and des and acrylates were similar to those of single amino acids.

] The ing effects were next evaluated. Ten out of 43 nds showed around 50% silencing at a dose of 1 mg/kg. The hit rate of the second set of compounds was 23%, which was over 10—fold more efficient compared to the first set of materials. The results suggested that our iterative screening process is an efficient strategy for identifying lead compounds. The results from the second set also showed that epoxide derivatives were more potent than aldehyde and acrylate derivatives (such as cKK—E12 vs cKK—A12 & cKK—Ol2).

Hit als were further tested at a lower dose of 0.1 mg/kg. The tail length significantly affects silencing and 12—14 carbon tail lengths appeared favorable (cKK—E10, —E12, —E14, & — E16). 2 was the most potent material and was selected for further exploration.

Biodistribution Study A biodistribution study was performed with naked Cy5.5 labeled siRNA and formulated cKK—E12. By subtracting the contribution of free siRNA in the formulation of cKK—E12, over 80% of particles were d in the liver at 1 hr and most residual siRNA was cleared by 24 hr through kidney (Figure 2).

Efi‘ects ofApolipoproteins on Cell Uptake and Gene Silencing Previous studies have reported that Apolipoprotein E (ApoE) was able to enhance cell uptake and gene silencing for a certain type of materials. Akinc, A., et al., Targeted delivery ofRNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol Ther. 18(7): p. 1357—64. In order to test the effects of diverse apoliproteins on cell uptake and gene silencing, and explore the mechanism of action, experiments were performed with cKK—E12 and ll ms of ApoA, ApoB, ApoC, ApoE, and ApoH. Results in Hela cells showed that most apolipoproteins did not affect cell viability with the exception of ApoB. ApoA, ApoC, and ApoH did not show significant effects on silencing compared to free cKK—E12 (Figure 3). However, four ent ApoE isoforms significantly ed rase silencing.

The activity of Z, cKK—AlZ, and cKK—012 was compared with and without addition of apoE3 (apoE3 is the dominant isoform in humans. Figure 4A). Without addition of ApoE3, cKK—A12 was more potent than cKK—E12 and cKK—OlZ. However, with addition of ApoE3, the order of silencing s was 2 > cKK—A12 > cKK—OlZ, which correlated well with in vivo activity. The results suggested that a cell assay with addition of ApoE might be a practical and effective model for preliminary screening for liver hepatocytes silencing. In addition, the cell uptake of cKK—E12 formulated with an Alexa— Fluor 647 labeled siRNA was visualized using automated confocal microscopy e 4B).

Other Embodiments In the claims articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are t in, employed in, or otherwise relevant to a given product or process unless ted to the contrary or otherwise evident from the t. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process.

The invention includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.

Furthermore, the invention encompasses all variations, ations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on r claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists, e. g., in Markush group format, each subgroup of the ts is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. It is also noted that the terms “comprising” and “containing” are intended to be open and permits the inclusion of onal elements or steps. Where ranges are given, endpoints are ed. Furthermore, unless ise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or nge within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patent applications, journal articles, books, manuals, and other publications, all of which are incorporated herein by reference. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular ment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Because such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein.

Any particular embodiment of the invention can be excluded from any claim, for any , whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ain using no more than routine experimentation many equivalents to the specific embodiments described . The scope of the present embodiments described herein is not intended to be limited to the above Description, but rather is as set forth in the appended claims. Those of ordinary skill in the art will iate that various changes and modifications to this description may be made without departing from the spirit or scope of the t invention, as defined in the following claims.

Claims

Claims (39)

What is claimed is:

1. A nd of Formula: or salt thereof; wherein: Q is O; each instance of R1 is ndently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, or a group of formula (iv), provided that at least one instance of R1 is a group of formula: (iv); L is an unsubstituted alkylene, optionally substituted lene, optionally tuted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, or optionally substituted heteroalkynylene; R6 and R7 are each independently a hydrogen, nitrogen protecting group, or a group of the formula (iii), provided that at least one instance of R6 and R7 is a group of the formula (iii); each instance of R2 is independently hydrogen, a nitrogen protecting group, or a group of the formula (iii); Formula (iii) is: (iii); provided formula (iii) is not a group of the formulae (i) or (ii): (i) (ii) wherein each instance of a (i) is independently formula (i-a) or formula (i-b): (i-a) (i-b); wherein: each ce of R′ is en; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, or a nitrogen protecting group; Y is O; RP is hydrogen or an oxygen protecting group; and RL is ally substituted C6-20 alkyl, ally substituted C6-20 alkenyl, ally substituted C6-20 alkynyl, optionally substituted heteroC6-20 alkyl, optionally substituted heteroC6- 20 alkenyl, optionally substituted C6-20 alkynyl; wherein “optionally substituted” refers to a carbon atom of a group which may be unsubstituted or independently substituted with halogen, –CN, –NO2, –N3, –SO2H, –SO3H, –OH, –ORaa, –N(Rbb)2, –SH, –SRaa, –SSRcc, –C(=O)Raa, –CO2H, –CHO, –CO2Raa, –OC(=O)Raa, – OCO2Raa, –C(=O)N(Rbb)2, –OC(=O)N(Rbb)2, –NRbbC(=O)Raa, –NRbbCO2Raa, – NRbbC(=O)N(Rbb)2, –C(=O)NRbbSO2Raa, –NRbbSO2Raa, –SO2N(Rbb)2, –SO2Raa, –SO2ORaa, – OSO2Raa, –S(=O)Raa, –OS(=O)Raa, –Si(Raa)3, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, C6–14 aryl, or 5–14 ed heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is ndently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; or two geminal hydrogens of the carbon atom are replaced with the group =O, =S, or =NRbb; or refers to a nitrogen atom of a group which may be unsubstituted or ndently substituted with –OH, –ORaa, –C(=O)Raa, –C(=O)N(Rcc)2, – CO2Raa, –SO2Raa, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from , sulfur, and nitrogen, C6–14 aryl, and 5–14 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from , sulfur, and nitrogen, or two Rcc groups attached to an N atom are joined to form a 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, , and nitrogen or 5–14 membered heteroaryl ring having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; each of Raa is ndently C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, C6–14 aryl, and 5–14 membered heteroaryl, or two Raa groups are joined to form a 3–14 membered heterocyclyl or 5–14 ed heteroaryl ring having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, wherein each alkyl, alkenyl, l, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; each of Rbb is independently hydrogen, –OH, –ORaa, –N(Rcc)2, –CN, Raa, – C(=O)N(Rcc)2, –CO2Raa, –SO2Raa,–SO2N(Rcc)2, –SO2Rcc, –SO2ORcc, –SORaa, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring atoms selected from oxygen, sulfur, and nitrogen, C6–14 aryl, or 5–14 membered aryl having ring carbon atoms and 1-4 ring atoms ed from oxygen, sulfur, and nitrogen, or two Rbb groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; each of Rcc is independently hydrogen, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, C6–14 aryl, or 5–14 ed heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, or two Rcc groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, yclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; each of Rdd is independently halogen, –CN, –NO2, –N3, –SO2H, –SO3H, –OH, –ORee, – N(Rff)2,–SH, –SRee, –SSRee, –C(=O)Ree, –CO2H, –CO2Ree, –OC(=O)Ree, –OCO2Ree, – C(=O)N(Rff)2, –OC(=O)N(Rff)2, –NRffC(=O)Ree, –NRffCO2Ree, –NRffC(=O)N(Rff)2,– NRffSO2Ree, –SO2N(Rff)2, e, ee, –OSO2Ree, –S(=O)Ree, –Si(Ree)3, C1–10 alkyl, C2– 10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–10 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from , sulfur, and nitrogen, C6–10 aryl, 5–10 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, wherein each alkyl, l, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups, or two geminal Rdd substituents can be joined to form =O; each of Ree is independently C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, C6–10 aryl, 3–10 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, and 5–10 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently tuted with 0, 1, 2, 3, 4, or 5 Rgg groups; each of Rff is independently hydrogen, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3–10 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, C6–10 aryl and 5–10 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, or two Rff groups are joined to form a 3–14 membered heterocyclyl or 5–14 membered heteroaryl ring, n each alkyl, alkenyl, l, carbocyclyl, heterocyclyl, aryl, and aryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups; each of Rgg is ndently n, –CN, –NO2, –N3, –SO2H, –SO3H, –OH, –OC1–10 alkyl, –N(C1–10 alkyl)2, –SH, –SC1–10 alkyl, –SS(C1–10 alkyl), (C1–10 alkyl), –CO2H, – CO2(C1–10 alkyl), –OC(=O)(C1–10 alkyl), –OCO2(C1–10 alkyl), NH2, –C(=O)N(C1–10 alkyl)2, )NH(C1–10 alkyl), –NHC(=O)( C1–10 alkyl), –N(C1–10 alkyl)C(=O)( C1–10 alkyl), –NHCO2(C1–10 alkyl), –NHC(=O)N(C1–10 alkyl)2, –NHC(=O)NH(C1–10 alkyl), –NHC(=O)NH2, –NHSO2(C1–10 alkyl), –SO2N(C1–10 alkyl)2, –SO2NH(C1–10 alkyl), –SO2NH2,–SO2C1–10 alkyl, – –10 alkyl, 1–6 alkyl, –SOC1–6 alkyl, –Si(C1–10 alkyl)3, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, C6–10 aryl, 3–10 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, 5–10 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen; or two geminal Rgg substituents can be joined to form =O; a nitrogen protecting group is selected from the group consisting of –OH, –ORaa, – N(Rcc)2, –C(=O)Raa, N(Rcc)2, –CO2Raa, –SO2Raa, –C(=NRcc)Raa, cc)ORaa, – C(=NRcc)N(Rcc)2, –SO2N(Rcc)2, –SO2Rcc, –SO2ORcc, –SORaa, –C(=S)N(Rcc)2, SRcc, – C(=S)SRcc, C1–10 alkyl, aralkyl, heteroaralkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 carbocyclyl, 3– 14 membered heterocyclyl, C6–14 aryl, and 5–14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, l, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, wherein Raa, Rbb, Rcc and Rdd are as defined ; an oxygen protecting group and a sulfur ting group are independently selected from the group consisting of –Raa, –N(Rbb)2, –C(=O)SRaa, Raa, –CO2Raa, –C(=O)N(Rbb)2, – C(=NRbb)Raa, –C(=NRbb)ORaa, –C(=NRbb)N(Rbb)2, –S(=O)Raa, –SO2Raa, and –Si(Raa)3, wherein Raa, Rbb, and Rcc are as defined herein.

2. The compound of claim 1, wherein at least one instance of R2 is hydrogen.

3. The nd of claim 1, wherein at least one instance of R2 is a group of formula (iii).

4. The compound of claim 1 or 2, wherein each R1 is a group of formula (iv).

5. The compound of any one of claims 1 to 4, wherein L is an unsubstituted alkylene.

6. The compound of any one of claims 1 to 5, wherein the group of formula (iv) is of formula: wherein q is an integer between 1 and 50, inclusive.

7. The compound of any one of claims 1 to 6, wherein the compound is selected from the group consisting of: , , , , , and , and salts thereof, wherein: p is 1; and each R1 independently is -H , -CH3, 3)2, -CH(CH3)(CH2CH3), - CH2CH(CH3)2, , , , , , , , , , , , , , , or , wherein R6 and R7 are each independently hydrogen, a en protecting group, or a group of formula (iii), provided that at least one instance of R6 and R7 is a group of the formula (iii); and provided that at least one R1 is a group of formula:

8. The compound of claim 1, wherein the compound is selected from the group consisting , , , , , , , , , , , , , , , , , , , and , and salts thereof, wherein p is 1; and ed that at least one instance of R2 is a group of the formula (iii).

9. The compound of claim 1, wherein the compound is: or salt thereof.

10. The compound of any one of claims 1 to 8, or salt thereof, wherein RL is optionally substituted C6-20 alkyl.

11. A ition comprising a compound of any one of claims 1 to 10, or salt thereof, and an excipient.

12. The composition of claim 11, wherein the composition is a pharmaceutical ition, a cosmetic composition, a nutraceutical composition, or a ition with non-medical application.

13. The composition of claim 12, wherein the composition with non-medical application is an emulsion or emulsifier useful as a food component, for extinguishing fires, for disinfecting surfaces, or for oil cleanup.

14. The composition of claim 11, wherein the composition is a pharmaceutical composition.

15. The composition of claim 11, wherein the ition further comprises cholesterol.

16. The composition of claim 11, wherein the composition further comprises a PEGylated lipid.

17. The ition of claim 11, n the composition further ses a phospholipid.

18. The composition of claim 11, wherein the composition further comprises an apolipoprotein.

19. The composition of claim 11, n the composition further ses an agent.

20. The composition of claim 19, wherein the agent is an organic molecule, inorganic molecule, nucleic acid, protein, peptide, polynucleotide, targeting agent, an isotopically labeled chemical compound, vaccine, an immunological agent, or an agent useful in bioprocessing.

21. The composition of claim 19, wherein the agent is a polynucleotide.

22. The composition of claim 21, wherein the polynucleotide is DNA or RNA.

23. The composition of claim 21, wherein the polynucleotide is RNA.

24. The composition of claim 23, wherein the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA.

25. The composition of claim 19, wherein the agent and the compound are not covalently attached.

26. The composition of claim 11, wherein the composition is in the form of a particle.

27. The ition of claim 26, wherein the particle is a nanoparticle or microparticle.

28. The composition of claim 26, wherein the particle is a micelle, liposome, or lipoplex.

29. The composition of claim 26, wherein the particle encapsulates an agent.

30. A method of screening a compound library, the method sing: providing a plurality of nds according to any one of claims 1 to 10, or salts thereof; and performing at least one assay with the compound library to determine the presence or e of a desired property; wherein the desired property is solubility in water, solubility at ent pH, ability to bind polynucleotides, ability to bind heparin, ability to bind small molecules, ability to bind protein, ability to form microparticles, ability to increase tranfection efficiency, ability to support cell growth, ability to support cell ment, ability to support tissue growth, and/or intracellular delivery of the compound and/or an agent complexed or attached thereto to aid in bioprocessing.

31. A compound according to any one of claims 1 to 10, or salt thereof, for use in treating a disease, er, or condition from which a subject suffers.

32. The compound of claim 31, wherein the disease, disorder, or ion is selected from the group consisting of proliferative disorders, inflammatory disorders, autoimmune disorders, painful conditions, liver diseases, and familial amyloid neuropathies.

33. Use of a compound according to any one of claims 1 to 9, or salt thereof, and a cleotide, in the manufacture of a pharmaceutical ition for delivering the polynucleotide to a cell.

34. The use of claim 33, wherein the polynucleotide is DNA.

35. The use of claim 33, wherein the polynucleotide is RNA.

36. The use of claim 35, wherein the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA.

37. The use of claim 35, wherein the polynucleotide is RNA, and upon delivery of the RNA into the cell, the RNA is able to interfere with the expression of a specific gene in the biological cell.

38. The composition of claim 21, wherein the cleotide encodes a protein or peptide.

39. The use of claim 33, wherein the polynucleotide s a protein or peptide. WO 63468