NZ733610B2 - 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. 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. , 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 DERIVATES FUNCTIONALIZED ON THE INAL CAPABLE OF FORMING DRUG INCAPSULATING MICROSPHERES Related Applications The present application claims priority under 35 U.S.C. § 119(e) to US. provisional patent ation, U.S.S.N. 61/552,423, filed October 27, 2011, which is incorporated herein by reference.

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

Background of the Invention The ability to silence genes via RNA erence (RNAi) was ed by Mello and Fire in 1998. See Fire et al., Nature (1998) 391:806—81 1. Since then, scientists have rushed to take advantage of the enormous therapeutic potential driven by targeted gene knockdown. This is evidenced 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 s. See Davis et al., Nature (2010) 464: 1067—1070. It is well understood that development of genetic drugs is slowed by the inability to deliver c 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 Reviews 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 mentary mRNA sequences, thereby preventing translation of the target mRNA into protein, i.e., “silencing” the gene.

To overcome difficulties in ry, nucleotides have been complexed with a wide variety of delivery s, 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. Respir. Crit. Care Med. (2011) 183:531—538), the clinical use of siRNA continues to require development of safer and more effective ry systems. Toward this end, numerous lipid—like molecules have been developed including poly B—amino esters and amino alcohol lipids. See, e. 57., PCT Application Publication Nos. ; ; ; ; WC 2006/138380; and . Amino acid, e, polypeptide—lipids (APPL) have also been studied for a variety of applications, ing use as therapeutics, biosurfactants, and nucleotide delivery systems. See, e. g., Giuliani et al., Cellular and Molecular Life Sciences (2011) 68:2255—2266; lkeda et al., t 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 improved APPL nucleotide delivery systems. y of the Invention Described herein are inventive compounds and compositions terized, in certain embodiments, by conjugation of various , such as lipophilic 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 ations, such as, for example, improved nucleotide delivery.

Exemplary APPLs include, but are not d 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 herein, 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) each instance of R’ is independently hydrogen or optionally substituted alkyl; X is O, S, NRX, wherein RX is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted yclyl, 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 tuted alkynyl, optionally tuted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally substituted 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 tuted aryl, ally 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 substituted heteroC1_50 alkyl, optionally substituted heteroC2_50 alkenyl, optionally substituted heteroC2_50 alkynyl, or a polymer.

In certain embodiments, the group of a (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 (i—a2): 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 a : R' IRL R' RL (i-bl) (i—b2) In certain embodiments, at least one instance of R1 is a group of formula: E—L—N R7 (iV) n L is an optionally substituted alkylene, ally substituted alkenylene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, optionally substituted yclylene, optionally substituted heterocyclylene, optionally substituted arylene, or optionally substituted heteroarylene, and R6 and R7 are independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, 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 substituted alkyl; X is O, S, NRX, wherein RX 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; Y is O, S, NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted l, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally substituted l, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally tuted heterocyclyl, ally 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 tuted C250 alkenyl, ally tuted 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 n 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): C10H21/S 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, ally, 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 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 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 n embodiments, the composition further comprises an agent. In certain embodiments, the agent is an organic molecule, inorganic molecule, nucleic acid, protein, peptide, polynucleotide, ing agent, an isotopically d chemical compound, vaccine, an immunological agent, or an agent useful bioprocessing, e.g., in the intracellular manufacturing of proteins. In certain embodiments, the agent is a polynucleotide, and the polynucleotide is DNA or RNA. In certain embodiments, the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA. In certain embodiments, the agent and the APPL are not ntly attached, e.g., for e, the agent and the APPL are valently complexed to each other. However, in n embodiments, the agent and the APPL are covalently attached.

In certain ments, the composition is in the form of a particle. In certain embodiments, the particle is a rticle or microparticle. In certain embodiments, the particle is a micelle, liposome, or lipoplex. In certain embodiments, the particle encapsulates an agent, 6.57., an agent to be delivered.

In r aspect, provided is a method of delivering a polynucleotide to a biological cell, sing 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 f, 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 n embodiments, upon delivery of the RNA into the cell, the RNA is able to ere with the expression of a specific gene in the biological cell.

In yet another aspect, provided are screening methods. For example, in one ment, 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 se 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 thereof, 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, 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 t cell growth, ability to support cell attachment, ability to support tissue growth, and/or intracellular delivery of the APPL and/or an agent complexed or ed o to aid in bioprocessing.

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

The s of one or more ments 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 .

Definitions Chemical definitions Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the ic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., inside cover, and specific functional groups are generally defined as bed therein. onally, l principles of organic chemistry, as well as specific functional 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 Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern s of Organic Synthesis, 3rd Edition, Cambridge University Press, Cambridge, 1987. nds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e. g., enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual omer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures ed in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred s 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 invention additionally encompasses compounds as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.

When a range of values is , 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 l of a straight—chain or branched saturated hydrocarbon 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 alkyl”). 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 ). 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), iso—butyl (C4), n—pentyl (C5), 3—pentanyl (C5), amyl (C5), neopentyl (C5), 3—methyl—2—butanyl (C5), tertiary amyl (C5), and n—hexyl (C6). onal examples of alkyl groups e n—heptyl (C7), n—octyl (C8) and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a ituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is an unsubstituted C150 alkyl. In certain ments, 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 , , nitrogen, boron, silicon, or phosphorus within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal on(s) of the parent chain. In certain embodiments, a heteroalkyl group refers to a saturated group haVing from 1 to 50 carbon atoms and l or more heteroatoms within the parent chain roCHo alkyl”).

In certain embodiments, a heteroalkyl group refers to a saturated group haVing from 1 to 40 carbon atoms and l or more atoms 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 embodiments, a alkyl 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 ted 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 ments, a heteroalkyl group is a ted 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 atoms Within the parent chain (“heteroCM alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 5 carbon atoms and l or 2 heteroatoms Within the parent chain (“heteroC1,5 alkyl”). In some ments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and lor 2 heteroatoms 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 heteroalkyl group is a saturated group having 1 to 2 carbon atoms and l heteroatom Within the parent chain (“heteroCH alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 carbon atom and l atom roC1 alkyl”). In some embodiments, 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 ndently unsubstituted (an “unsubstituted heteroalkyl”) or substituted (a “substituted heteroalkyl”) with one or more substituents. In certain embodiments, the heteroalkyl group is an unsubstituted heteroC1,50 alkyl. In certain embodiments, the heteroalkyl group is a substituted heteroC1,50 alkyl.

As used herein, “alkenyl” refers to a radical of a ht—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 alkenyl 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 l”). 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 l 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 alkenyl”). 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 2—butenyl) or terminal (such as in l— l). Examples of C24 alkenyl groups include ethenyl (C2), l—propenyl (C3), 2—propenyl (C3), l—butenyl (C4), 2—butenyl (C4), butadienyl (C4), and the like. Examples of C24 alkenyl groups include 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 ise specified, each ce of an alkenyl group is independently unsubstituted (an “unsubstituted alkenyl”) or tuted (a “substituted alkenyl”) with one or more substituents. In certain embodiments, the alkenyl group is an unsubstituted C240 alkenyl. In certain embodiments, the alkenyl group is a substituted C240 l.

As used herein, “heteroalkenyl” refers to an alkenyl group as d 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, en, 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 certain 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 alkenyl”). In certain ments, a heteroalkenyl group refers to a group haVing from 2 to 30 carbon atoms, at least one double bond, and l or more atoms 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 embodiments, 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 l”). 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 specified, each instance of a alkenyl group is independently unsubstituted (an “unsubstituted heteroalkenyl”) or substituted (a “substituted heteroalkenyl”) with one or more substituents. In certain embodiments, the heteroalkenyl group is an tituted C2,50 alkenyl. In certain embodiments, the heteroalkenyl group is a substituted heteroC2,50 alkenyl.

As used herein, “alkynyl” refers to a radical of a straight—chain or branched hydrocarbon group haVing from 2 to 50 carbon atoms and one or more —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 l group that has one or more triple bonds and one or more double bonds is also referred to as an “ene—yene”. 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 alkynyl 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 l group has 2 to 6 carbon atoms (“C24 alkynyl”).

In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C2,5 l”). 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 l”). 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 alkynyl groups e, Without limitation, ethynyl (C2), l—propynyl (C3), 2—propynyl (C3), l—butynyl (C4), 2—butynyl (C4), and the like. Examples of C24 alkenyl 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 tuted C250 alkynyl.

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 oxygen, sulfur, nitrogen, boron, n, 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 alkynyl 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 roC2,50 alkynyl”). In certain embodiments, a alkynyl 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 ments, 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 (“heteroCHo alkynyl”). In certain embodiments, a heteroalkynyl 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 l”). 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 (“heteroCHo alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 9 carbon atoms, at least one triple bond, and l or more atoms 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 embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and l or more heteroatoms 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 ments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and lor 2 atoms within the parent chain (“heteroC24 alkynyl”). In some embodiments, a heteroalkynyl group has 2 to 3 carbon atoms, at least one triple bond, and l heteroatom within the parent chain (“heteroCH 2012/062222 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 specified, each instance of a heteroalkynyl group is independently unsubstituted (an “unsubstituted heteroalkynyl”) or substituted (a “substituted heteroalkynyl”) with one or more substituents. In certain embodiments, the heteroalkynyl group is an unsubstituted heteroC2,50 l. In certain embodiments, the heteroalkynyl group is a substituted C2,50 alkynyl.

As used , cyclyl” or cyclic” refers to a l 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 embodiments, 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 yclyl”). In some embodiments, a carbocyclyl group has 4 to 6 ring carbon atoms (“C44 carbocyclyl”). In some embodiments, a carbocyclyl 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 include, without limitation, cyclopropyl (C3), cyclopropenyl (C3), cyclobutyl (C4), cyclobutenyl (C4), cyclopentyl (C5), cyclopentenyl (C5), cyclohexyl (C6), cyclohexenyl (C6), cyclohexadienyl (C6), and the like. Exemplary C34; carbocyclyl groups include, without tion, the aforementioned C34 yclyl groups as well as cycloheptyl (C7), cycloheptenyl (C7), cycloheptadienyl (C7), cycloheptatrienyl (C7), cyclooctyl (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 onyl (C9), cyclononenyl (C9), cyclodecyl (C10), cyclodecenyl (C10), octahydro—lH—indenyl (C9), decahydronaphthalenyl (C10), 4.5]decanyl (C10), and the like. As the foregoing examples illustrate, in certain 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 n the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring . Unless otherwise specified, each instance of a carbocyclyl group is independently unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents. In certain embodiments, the carbocyclyl group is an unsubstituted C340 carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C340 carbocyclyl.

In some embodiments, cyclyl” 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 cycloalkyl”). Examples of C54 lkyl groups include cyclopentyl (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 cycloalkyl group is an unsubstituted C340 cycloalkyl. In certain embodiments, the lkyl group is a substituted C340 cycloalkyl.

As used , “heterocyclyl” or “heterocyclic” refers to a radical of a 3— to l4—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, nitrogen, boron, n, or phosphorus (“3—14 membered heterocyclyl”). In cyclyl groups that contain one or more nitrogen 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 heterocyclyl”)), and can be saturated or can n one or more carbon—carbon double or triple bonds. cyclyl polycyclic ring systems can e one or more heteroatoms in one or both rings. “Heterocyclyl” also es ring systems wherein the heterocyclyl ring, as d above, is fused with one or more yclyl groups wherein the point of attachment is either on the yclyl or heterocyclyl ring, or ring systems wherein the cyclyl 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 otherwise specified, each instance of heterocyclyl is independently unsubstituted (an “unsubstituted cyclyl”) 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 ments, a heterocyclyl 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, sulfur, nitrogen, boron, silicon, or phosphorus (“5—10 membered 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 atoms, wherein each heteroatom is independently selected from oxygen, sulfur, nitrogen, boron, n, or phosphorus (“5—8 membered heterocyclyl”). In some embodiments, 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, n each heteroatom is independently selected from oxygen, sulfur, en, boron, n, or phosphorus (“5—6 membered heterocyclyl”). In some ments, the 5—6 membered heterocyclyl 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 cyclyl has 1 or 2 ring heteroatoms selected from oxygen, sulfur, nitrogen, boron, n, 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 heteroatom include, without limitation, azirdinyl, oxiranyl, thiorenyl. Exemplary 4—membered heterocyclyl groups containing 1 heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5—membered heterocyclyl groups containing 1 heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl—2,5—dione. ary 5— membered heterocyclyl groups ning 2 heteroatoms include, without limitation, dioxolanyl, oxathiolanyl and dithiolanyl. Exemplary 5—membered heterocyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6—membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyl, ydropyranyl, dihydropyridinyl, and thianyl.

Exemplary 6—membered heterocyclyl groups containing 2 heteroatoms include, without limitation, zinyl, morpholinyl, dithianyl, dioxanyl. Exemplary 6—membered heterocyclyl groups containing 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, yl and nyl.

Exemplary bicyclic heterocyclyl groups include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, ydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, drochromenyl, octahydroisochromenyl, decahydronaphthyridinyl, decahydro—l ,8—naphthyridinyl, octahydropyrrolo[3,2—b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyl, zo[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— b]pyridinyl, 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 embodiments, an aryl group has 10 ring carbon atoms (“C10 aryl”; e.g., yl 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 . Unless otherwise specified, each instance of an aryl group is ndently unsubstituted (an stituted 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 substituted C644 aryl.

As used herein, “heteroaryl” refers to a radical of a 5—14 membered clic or clic (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 ic ring system, 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 include 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 s continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as d above, is fused with one or more aryl groups wherein the point of attachment 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 heteroatom (e.g., l, quinolinyl, carbazolyl, 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 membered aromatic ring system having ring carbon atoms and l or more (e.g., l, 2, 3, or 4) ring heteroatoms ed in the aromatic ring system, n each heteroatom is independently selected from oxygen, sulfur, nitrogen, boron, n, or phosphorus (“5—10 membered heteroaryl”). In some embodiments, 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 ed in the aromatic ring system, wherein each heteroatom is independently selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus (“5—8 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5—6 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 independently selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus (“5—6 membered heteroaryl”). In some ments, the 5—6 membered heteroaryl has 1 or more (e.g., l, 2, or 3) ring atoms selected from oxygen, sulfur, nitrogen, boron, silicon, or phosphorus. In some embodiments, the 5—6 ed heteroaryl has 1 or 2 ring atoms selected from oxygen, sulfur, 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 phosphorus. Unless otherwise specified, each instance of a heteroaryl group is independently unsubstituted (an “unsubstituted heteroaryl”) or substituted (a ituted heteroaryl”) with one or more substituents. In certain embodiments, the aryl group is an tituted 5—14 membered heteroaryl. In certain embodiments, the heteroaryl group is a substituted 5—14 membered aryl.

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

As used herein, the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term “partially unsaturated” is ed 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 ns all single bonds.

Affixing the suffix “—ene” to a group indicates the group is a divalent moiety, e.g., alkylene is the divalent moiety of alkyl, alkenylene is the divalent moiety of alkenyl, 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 arylene is the divalent moiety of heteroaryl.

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

Exemplary carbon atom substituents include, 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°°, Raa, —C02H, —CHO, —C(OR°°)2, — , —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, Rbb)N(Rbb)2, —NRbbC(=NRbb)N(Rbb)2, — C(=O)NRbbSOZRaa, —NRbb802Raa, —SOZN(Rbb)2, —sozRaa, 502011”, —osozRaa, —S(=0)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, >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, carbocyclyl, 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 instance of Raa is, independently, selected from C140 alkyl, C240 alkenyl, C250 alkynyl, 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, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, l, 2, 3, 4, or 5 Rdd groups; each ce of Rbb is, independently, selected from hydrogen, —OH, —ORaa, — N(RC°)2, —CN, —C(=O)Raa, —C(=O)N(R°C)2, —C02Raa, —SOzRaa, —C(=NR°°)ORaa, — C(=NR°°)N(R°°)2, —SOZN(RCC)2, —SOZR°°, —SOZOR°°, —SORaa, —C(=S)N(R°°)2, —C(=O)SR°°, — C(=S)SRCC, —P(=O)2Raaa —P(=O)(Raa)2, —P(=O)2N(RCC)2, (NRCC)2, C1750 alkyl, C2750 alkenyl, C240 alkynyl, C340 yclyl, 3—l4 membered heterocyclyl, C644 aryl, and 5—14 membered 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 ce of RCC is, independently, ed from en, C150 alkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—l4 membered heterocyclyl, C644 aryl, and 5—14 membered aryl, or two RCC groups are joined to form a 3—14 membered cyclyl 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 ce of Rdd is, independently, selected from halogen, —CN, —N02, —N3, — SOZH, —SO3H, —OH, —0Ree, —ON(Rff)2, —N(Rff)2, —N(Rff)3+X’, —N(ORee)Rff, —SH, —SRee, — SSRee, —C(=0)Ree, —C02H, —C02Ree, —0C(=0)Ree, —ocozRei —C(=O)N(Rff)2, — OC(=O)N(Rff)2, (=O)Ree, OZRee, (=O)N(Rff)2, —C(=NRff)ORee, — OC(=NRff)Ree, —OC(=NRff)ORee, —C(=NRff)N(Rff)2, —OC(=NRff)N(Rff)2, — 2012/062222 NRffC(=NRff)N(Rff)2,—NRffSOzRee, —SOZN(Rff)2, —sozRee, 50201166, —osozRee, Ree, —Si(Ree)3, —OSi(Ree)3, —C(=S)N(Rff)2, —C(=O)SRee, 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 membered heterocyclyl, C640 aryl, 5—10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and aryl is ndently 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, ed from C140 alkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, CMO aryl, 3—10 ed 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 alkynyl, C340 carbocyclyl, 3—10 membered heterocyclyl, C640 aryl and 5—10 membered heteroaryl, or two Rff 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 Rgg groups; and each instance of Rgg is, independently, halogen, —CN, —N02, —N3, —SOZH, —SO3H, — OH, 0 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, 0 alkyl, —SS(C1,50 alkyl), —C(=O)(C1,50 alkyl), —C02H, — C02(C1,50 alkyl), —OC(=O)(C1,50 alkyl), —OC02(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 alkyl), —NHC02(C1,50 alkyl), —NHC(=O)N(C1,50 alkyl)2, —NHC(=O)NH(C1,50 alkyl), — NHC(=O)NH2, —C(=NH)O(C1,50 alkyl),—OC(=NH)(C1,50 alkyl), —OC(=NH)OC1,50 alkyl, — C(=NH)N(C1,50 alkyl)2, —C(=NH)NH(C1,50 alkyl), )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, —NHSOZ(C1,50 alkyl), C1,50 alkyl)2, —SOZNH(C1,50 alkyl), — ,—SOZC1,50 alkyl, —SOZOC1,50 alkyl, —OSOZC14 alkyl, —SOC1,6 alkyl, —Si(C1,50 alkyl)3, 14 3 —C(=S)N(C1,50 2, C(=S)NH(C1,50 alkyl), C(=S)NH2, — 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 2, —OP(=O)(C1,50 alkyl)2, —OP(=O)(OC1,50 alkyl)2, C150 alkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, C640 aryl, 3—10 ed heterocyclyl, 5—10 membered heteroaryl; or two geminal 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 lity. Exemplary counterions include halide ions (e.g., F Cl Br I , , ), N03 OH , , C104 , , H2P04’, H8047, sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p—toluenesulfonate, benzenesulfonate, lO—camphor sulfonate, alene—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). en atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms. Exemplary nitrogen atom substitutents e, but are not limited to, hydrogen, —OH, —ORaa, —N(R°°)2, —CN, — C(=0)Raa, N(RCC)2, —C02Raa, —sozRaa, bb)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)SRCC, —P(=O)2Raaa —P(=O)(Raa)2, —P(=O)2N(RCC)2, —P(=O)(NRCC)2, C1750 alkyl, C2750 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—14 membered heterocyclyl, C644 aryl, and 5—14 membered heteroaryl, or two RCC groups ed to an N atom are joined to form a 3—14 membered heterocyclyl or 5—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, and wherein R”, Rbb, RCC and Rdd are as d above.

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, — 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 oalkyl, C240 alkenyl, C240 alkynyl, C340 carbocyclyl, 3—14 membered heterocyclyl, C644 aryl, and 5—14 membered heteroaryl, or two RCC groups attached to a nitrogen atom are joined to form a 3—14 membered heterocyclyl or 5—14 ed heteroaryl ring, wherein each alkyl, l, alkynyl, carbocyclyl, cyclyl, 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 embodiments, the tuent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group). Nitrogen protecting groups include, but are not d to, —OH, —ORaa, —N(R°°)2, Raa, —C(=O)N(R°C)2, a, —SOgRaa, —C(=NR°°)Raa, —C(=NR°°)ORaa, —C(=NR°°)N(R°°)2, —SOzN(R°°)2, —SOgR°°, — C, —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 heterocyclyl, C644 aryl, and 5—14 membered heteroaryl groups, n each alkyl, alkenyl, alkynyl, 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 e those described 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 reference.

For example, nitrogen protecting groups such as amide groups (e.g., — C(=O)Raa) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, roacetamide, phenylacetamide, 3—phenylpropanamide, picolinamide, 3—pyridylcarboxamide, N—benzoylphenylalanyl derivative, benzamide, p— phenylbenzamide, 0—nitophenylacetamide, 0—nitrophenoxyacetamide, acetoacetamide, (N’— dithiobenzyloxyacylamino)acetamide, 3—(p—hydroxyphenyl)propanamide, 3—(0— nitrophenyl)propanamide, 2—methyl—2—(0—nitrophenoxy)propanamide, 2—methyl—2—(0— phenylazophenoxy)propanamide, robutanamide, 3—methyl—3—nitrobutanamide, 0— nitrocinnamide, N—acetylmethionine derivative, 0—nitrobenzamide and 0— (benzoyloxymethyl)benzamide. en protecting groups such as carbamate groups (e.g., —C(=O)ORaa) include, but are not limited to, methyl carbamate, ethyl carbamante, 9—fluorenylmethyl carbamate (Fmoc), 9—(2—sulfo)fluorenylmethyl carbamate, 9—(2,7—dibromo)fluoroenylmethyl carbamate, 2,7 di t butyl [9 (10,10 dioxo 10,10,10,10—tetrahydrothioxanthyl)]methyl carbamate (DBD—Tmoc), 4—methoxyphenacyl carbamate (Phenoc), 2,2,2—trichloroethyl carbamate (Troc), 2—trimethylsilylethyl carbamate (Teoc), 2—phenylethyl carbamate (hZ), 1— (1—adamantyl)—1—methylethyl carbamate (Adpoc), 1,1—dimethyl—2—haloethyl ate, 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 ate (Bpoc), 1—(3,5—di—t— henyl)—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 carbamate (Alloc), 1— isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4—nitrocinnamy1 carbamate (Noe), 8—quinoly1 carbamate, N—hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p—methoxybenzyl carbamate (Moz), p—nitobenzyl carbamate, 1)— bromobenzyl carbamate, p—chlorobenzyl carbamate, chlorobenzy1 carbamate, 4— methylsulfinylbenzyl carbamate (Msz), 9—anthry1methy1 carbamate, diphenylmethyl carbamate, 2—methy1thioethy1 carbamate, 2—methy1sulfony1ethy1 carbamate, 2—(p— toluenesulfony1)ethy1 ate, [2—(1,3—dithiany1)]methy1 carbamate (Dmoc), 4— methylthiophenyl carbamate (Mtpc), 2,4—dimethy1thiopheny1 carbamate (Bmpc), 2— phosphonioethyl carbamate (Peoc), 2—tripheny1phosphonioisopropyl carbamate , 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— heny1)methy1 carbamate, t—amyl carbamate, S—benzyl rbamate, p—cyanobenzyl carbamate, utyl carbamate, exyl carbamate, cyclopentyl carbamate, cyclopropylmethyl ate, p—decyloxybenzyl carbamate, 2,2—dimethoxyacy1viny1 ate, 0—(N,N—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 ate, 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 carbamate, 1—methy1—1—pheny1ethy1 carbamate, 1— methyl—l—(4—pyridy1)ethy1 carbamate, phenyl carbamate, p—(phenylazo)benzy1 carbamate, 2,4,6—tri—t—butylpheny1 carbamate, 4—(trimethy1ammonium)benzy1 carbamate, and 2,4,6— trimethylbenzyl ate. en ting groups such as sulfonamide groups (e.g., —S(=O)2Raa) include, but are not limited to, p—toluenesulfonamide (Ts), esulfonamide, 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), methoxy—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, romethylsulfonamide, and phenacylsulfonamide.

Other en protecting groups include, but are not limited to, phenothiazinyl—(lO)—acyl derivative, N’—p—toluenesulfonylaminoacyl derivative, N’— phenylaminothioacyl derivative, N—benzoylphenylalanyl derivative, ylmethionine derivative, 4,5—diphenyl—3—oxazolin—2—one, N—phthalimide, N—dithiasuccinimide (Dts), N— 2,3—diphenylmaleimide, N—2,5—dimethylpyrrole, N—l , l ,4,4— tetramethyldisilylazacyclopentane adduct SE), 5—substituted l,3—dimethyl—l,3,5— triazacyclohexan—2—one, tituted l,3—dibenzyl—l,3,5—triazacyclohexan—2—one, l— substituted 3,5—dinitro—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— thoxyphenyl)diphenylmethyl]amine (MMTr), N—9—phenylfluorenylamine (PhF), N— 2,7—dichloro—9—fluorenylmethyleneamine, N—ferrocenylmethylamino (ch), N—2— picolylamino de, 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 tive, 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 present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl ting group). Oxygen protecting groups include, but are not limited to, —Raa, —N(Rbb)2, SRaa, —C(=0)Raa, —C02Raa, — C(=O)N(Rbb)2, —C(=NRbb)Raa, bb)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, —P<=0><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 described in detail in ting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference. ary oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t—butylthiomethyl, (phenyldimethylsilyl)methoxymethyl , benzyloxymethyl (BOM), p— methoxybenzyloxymethyl (PMBM), (4—methoxyphenoxy)methyl ), guaiacolmethyl (GUM), xymethyl, 4—pentenyloxymethyl (POM), siloxymethyl, 2— methoxyethoxymethyl (MEM), 2,2,2—trichloroethoxymethyl, bis(2—chloroethoxy)methyl, 2— (trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3— bromotetrahydropyranyl, tetrahydrothiopyranyl, l—methoxycyclohexyl, 4— methoxytetrahydropyranyl (MTHP), 4—methoxytetrahydrothiopyranyl, 4— methoxytetrahydrothiopyranyl S,S—dioxide, l—[(2—chloro—4—methyl)phenyl]—4— methoxypiperidin—4—yl (CTMP), l,4—dioxan—2—yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a—octahydro—7,8,8—trimethyl—4,7—methanobenzofuran—2—yl, l—ethoxyethyl, l—(2—chloroethoxy)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), oxybenzyl, 3,4—dimethoxybenzyl, 0—nitrobenzyl, p—nitrobenzyl, p— halobenzyl, 2,6—dichlorobenzyl, p—cyanobenzyl, p—phenylbenzyl, 2—picolyl, 4—picolyl, 3— methyl—2—picolyl N—oxido, diphenylmethyl, p,p ’—dinitrobenzhydryl, 5—dibenzosuberyl, nylmethyl, (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, ryl, 9—(9—phenyl)xanthenyl, 9—(9—phenyl— lO—oxo)anthryl, l,3—benzodisulfuran—2—yl, benzisothiazolyl S,S—dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, t—butyldimethylsilyl (TBDMS), t— butyldiphenylsilyl (TBDPS), tribenzylsilyl, xylylsilyl, triphenylsilyl, ylmethylsilyl (DPMS), t—butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, rophenoxyacetate, 3— phenylpropionate, 4—oxopentanoate (levulinate), 4,4—(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4—methoxycrotonate, benzoate, p— phenylbenzoate, 2,4,6—trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9— fluorenylmethyl ate (Fmoc), alkyl ethyl carbonate, alkyl trichloroethyl carbonate (Troc), 2—(trimethylsilyl)ethyl carbonate (TMSEC), 2—(phenylsulfonyl) ethyl carbonate (Psec), 2—(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl Vinyl carbonate alkyl allyl carbonate, alkyl p—nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p—methoxybenzyl ate, alkyl 3,4—dimethoxybenzyl carbonate, alkyl 0—nitrobenzyl carbonate, alkyl p—nitrobenzyl carbonate, alkyl S—benzyl thiocarbonate, 4—ethoxy—l— napththyl carbonate, methyl dithiocarbonate, benzoate, 4—azidobutyrate, 4—nitro—4— methylpentanoate, 0—(dibromomethyl)benzoate, ylbenzenesulfonate, 2— (methylthiomethoxy)ethyl, hylthiomethoxy)butyrate, 2— (methylthiomethoxymethyl)benzoate, 2,6—dichloro—4—methylphenoxyacetate, 2,6—dichloro— 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, e, alkyl N,N,N’,N’— tetramethylphosphorodiamidate, alkyl N—phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4—dinitrophenylsulfenate, sulfate, esulfonate (mesylate), benzylsulfonate, and tosylate (Ts).

In certain embodiments, the substituent present on an sulfur atom is an sulfur protecting group (also referred to as a thiol protecting group). Sulfur protecting groups e, but are not limited to, —Raa, —N(Rbb)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)3, )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 . Sulfur protecting groups are well known in the art and include those described 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 reference.

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

These and other exemplary substituents are described in more detail in the Detailed ption, Examples, Figures, and Claims. The invention is not intended 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 ral 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 peptide 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 depicted herein; see, e.g., Table l of the es.

As used herein, a “polymer” refers to a nd 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, “lipophilic” refers to the ability of a group to dissolve in fats, oils, lipids, and lipophilic non—polar solvents such as hexane or toluene. In general, a lipophilic group refers to an unsubstituted n—alkyl or unsubstituted nyl 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 tural isomer,77 nic molecule,” and “inorganic molecule” are meant to encompass the common meaning of each term as known in the art.

As used herein, 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, ive). In certain embodiments, the small organic molecule is a therapeutically active agent such as a drug (e.g., a small organic molecule 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 organometallic le.” As used herein, a “large organic molecule” or “large molecule” refers to an organic compound with a molecular weight of r than 800 g/mol (e.g., r 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, ive, between 1000 to 2000 g/mol, inclusive, or between 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 organic molecule approved by the US. Food and Drug Administration as provided in the Code of l Regulations (CFR)).The large organic molecule may also be complexed with a metal.

In this instance, the large c molecule is also ed to as an “large organometallic compound.” As used herein, a “small inorganic molecule” refers to an inorganic 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 nic molecule is a therapeutically active agent such as a drug (e.g., a small inorganic molecule approved by the US. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)).

As used , 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, inclusive). In certain embodiments, the large inorganic 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 provided in the Code of Federal Regulations (CFR)).

As used herein, the term “salt” or aceutically acceptable salt” refers to those salts which are, within the scope of sound medical nt, suitable for use in contact with the s of humans and lower animals without undue toxicity, 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 es (1977) 66: 1—19. ceutically acceptable salts of the nds of this invention include those derived from suitable inorganic and c acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and oric 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 adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, odide, 2—hydroxy—ethanesulfonate, ionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2— naphthalenesulfonate, nicotinate, e, oleate, oxalate, palmitate, pamoate, pectinate, fate, 3—phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p—toluenesulfonate, undecanoate, valerate salts, and the like.

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

Brief Description of the Drawings Figure 1 depicts the ural 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 igated 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 , E: epoxide, A: aldehyde, 0: acrylate, 12: carbon tail length. cKK— E12; c: cyclic; Control, phosphate—buffered saline.

Figure 2 depicts the stribution 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 effects of apolipoproteins on cKK—E12 in HeLa cells. Apolipoproteins including ApoA—I (recombinant Human ApoA—I protein), ApoA—II (native Human ApoA—II protein), ApoB (native Human ApoB n), ApoC—I (native Human ApoC—I protein), ApoC—II (native Human ApoC—II protein), ApoC—III e Human ApoC—III 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 cKK—012 in vitro : 50 ng/well). With addition of ApoE, the order of silencing effects was cKK—E12 > cKK—A12 > cKK—OlZ, correlating well with in vivo activity. B). Cellular internalization of cKK—E12 with 47 labeled siRNA after 3 hr of tion is demonstrated by HT automated al copy. ApoE enhanced cell uptake and endosomal escape of cKK—E12; Scale bar: 20 Detailed Description of Certain Embodiments of the Invention Described herein are inventive compounds and itions, certain embodiments of which involve conjugation of various groups, such as lipophilic groups, to an amino or amide group of an amino acid, a linear or cyclic peptide, a linear or cyclic polypeptide, or structural isomer f, 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 delivery. ary 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 ary amino group or amide of the amino acid, peptide, or polypeptide precursor, or structural isomer thereof, with an epoxide, thiirane, or aziridine of formula (i—X), Michael on to an OL,B—unsaturated ester, thioester, or amide of formula (ii— X), or reductive ion to an aldehyde of formula (iii—X) (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 certain ments, compounds of Formula (I), (II), (III), (IV), (V), and (VI), comprising at least one instance of a group attached thereto of the formula: H\ R'- RI $4 (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 tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen ting group; Y is O, S, NRY, wherein RY is hydrogen, optionally tuted alkyl, optionally substituted l, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, optionally tuted alkenyl, ally substituted l, optionally substituted carbocyclyl, ally 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 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 heteroalkenyl, optionally substituted C250 heteroalkynyl, or a polymer.

Various embodiments of formula (i), (ii), and (iii), and variables 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 nitrogen, of a group of formula (i), (ii), or (iii).

WO 63468 2012/062222 imino nitrogens Thus, in one aspect, provided is a compound of Formula (I): ” (I) or salt thereof; wherein: n is 0 or is an r 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, ally 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 l, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1; wherein each ence of RAl is independently hydrogen, optionally tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen 2012/062222 protecting group when attached to an oxygen atom, a sulfur protecting 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 cyclic or optionally substituted heteroaryl ring; R2 is a group of formula (i), (ii), or (iii); R3 is hydrogen, ally 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); or R3 and an R1 group are joined to form an optionally tuted 5—6 membered heterocyclic ring; R4 is —ORA4, —N(RA4)2, or —SRA4; wherein each occurrence of RA4 is ndently 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 an sulfur atom, a nitrogen protecting group when attached to a nitrogen atom, or two RA4 groups are joined to form an optionally tuted heterocyclic or optionally substituted aryl ring; R5 is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, 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 alkynyl, optionally substituted carbocyclyl, optionally tuted heterocyclyl, optionally tuted 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 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 tuted 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 ting group when attached to a nitrogen atom; and RL is optionally substituted C150 alkyl, optionally substituted C250 l, optionally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally substituted C2_50 alkenyl, optionally substituted heteroC2_50 alkynyl, or a r.

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

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

In certain embodiments, wherein n is 0 and Z is 0, one or more of the following 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 f; 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 100,000, inclusive. It is thus understood that Formula (I) asses amino acids ated to a lipid group, as well as linear peptides and linear polypeptides conjugated to lipid groups.

In certain embodiments, n is 0 or is an integer between 1 and 90,000, ive.

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 certain 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 integer between 1 and 30,000, inclusive. In certain ments, n is 0 or is an integer between 1 and 20,000, inclusive. In certain embodiments, 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 r 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 n 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, ive. In n 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 n embodiments, n is 0 or is an r between 1 and 900, inclusive. In certain embodiments, n is 0 or is an r between 1 and 800, inclusive. In certain embodiments, n is 0 or is an integer n 1 and 700, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 600, inclusive. In certain embodiments, n is 0 or is an integer between 1 and 500, inclusive. In certain embodiments, n is 0 or is an integer between 100 and 80,000, inclusive. In n embodiments, n is 0 or is an integer between 200 and 80,000, inclusive.

In certain embodiments, n is 0 or is an integer between 300 and 80,000, inclusive. In certain embodiments, n is 0 or is an r between 400 and 80,000, inclusive. In certain embodiments, n is 0 or is an r between 500 and , 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 , inclusive. In certain embodiments, n is 0 or is an integer between 1 and 400, inclusive. In n embodiments, n is 0 or is an integer between 1 and 300, inclusive. In certain embodiments, n is 0 or is an r 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 r 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 integer between 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 thereof.

In certain embodiments, when n is l, the compound 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 Formula (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 nd of Formula (I) is a compound of the a (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 compound of a (I) is a compound of the Formula (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 certain embodiments, each instance of m is 1. In certain 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 embodiments, at least one instance of R’ is hydrogen.

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

As lly defined above, each instance of Z is independently O, S, or NRZ, wherein RZ 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 a (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 certain embodiments, each instance of Z is S.

In certain embodiments, at least one instance of Z is NRZ. In certain embodiments, each instance of Z is NRZ. In certain embodiments, each instance of RZ 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, optionally substituted alkenyl, optionally substituted alkynyl, ally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted 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 tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

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

In certain embodiments, at least one ce of R1 is optionally substituted alkenyl, e.g., optionally substituted C2_6alkenyl, optionally substituted C3_6alkenyl, optionally substituted C4_6alkenyl, ally substituted C4_5alkenyl, or optionally 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, ally substituted kynyl, or ally substituted 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 tuted heterocyclyl, e.g., ally substituted 3—14 membered heterocyclyl, optionally tuted 3—10 membered heterocyclyl, optionally substituted 5—8 membered heterocyclyl, optionally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered cyclyl, 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 heteroaryl, optionally substituted 5—6 membered heteroaryl, optionally substituted membered heteroaryl, or ally substituted 6 membered heteroaryl.

] In any of the above embodiments, the R1 alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl group may be tuted, 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 instance of R6 and R7 is independently hydrogen, optionally tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted yclyl, 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).

For example, in certain embodiments, at least one instance of R1 is an alkyl, alkenyl, alkynyl, yclyl, heterocyclyl, aryl, or heteroaryl group tuted 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: L is an optionally substituted alkylene, ally substituted lene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, optionally tuted 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 tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted 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): . 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 formula (iv).

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

In certain ments, 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, ally substituted C1_6alkylene, optionally substituted C2- 6alkylene, ally substituted C3_6alkylene, optionally substituted C4_6alkylene, ally 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, ally substituted C4- nylene, optionally substituted C6_20alkenylene, optionally substituted Cg_20all<enylene, optionally tuted C10_20alkenylene, optionally substituted C2_6alkenylene, ally substituted C3_6alkenylene, ally substituted C4_6alkenylene, optionally substituted C4- 5alkenylene, or optionally substituted 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, optionally substituted Cnoalkynylene, optionally substituted C4- goalkynylene, optionally substituted C6_20alkynylene, optionally substituted Cg_20all<ynylene, optionally substituted C10_20alkynylene, optionally substituted C2_6alkynylene, ally substituted C3_6alkynylene, optionally substituted C4_6alkynylene, optionally substituted C4- 5alkynylene, or optionally substituted C3_4alkynylene.

In certain embodiments, L is an optionally tuted heteroalkylene; e.g., optionally substituted C1_50alkylene, optionally substituted heteroC1_40alkylene, optionally tuted 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 substituted heteroC4_6alkylene, optionally substituted C4_5alkylene, or optionally substituted heteroC3_4alkylene.

In certain ments, L is an optionally substituted heteroalkenylene, e.g., optionally substituted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, optionally substituted heteroC2_30alkenylene, optionally substituted C2_20alkenylene, optionally substituted heteroC4_20alkenylene, optionally substituted heteroC6_20alkenylene, optionally substituted heterng_20all<enylene, optionally substituted heteroC10_20alkenylene, ally substituted heteroC2_6alkenylene, ally substituted C3_6alkenylene, optionally substituted heteroC4_6alkenylene, ally substituted heteroC4_5alkenylene, or optionally substituted C3_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 tuted C2_20alkynylene, optionally substituted heteroC4_20alkynylene, optionally substituted C6_20alkynylene, optionally substituted heterng_20alkynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, optionally substituted C3_6alkynylene, optionally substituted heteroC4_6alkynylene, optionally substituted heteroC4_5alkynylene, or optionally substituted heteroC3_4alkynylene.

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

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., ally substituted 5— l4 membered heteroarylene, optionally substituted 5—10 membered heteroarylene, 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 formula (iv) is a group of the formula: wherein q is an r 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, ive. In certain embodiments, q is an integer between 8 and 20, ive. In n 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 ments, q is 9. In n embodiments, q is 10.

In certain embodiments, both R6 and R7 are hydrogen. In certain embodiments, R6 is en 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 certain ments, both R6 and R7 are independently a group of the formula (i), (ii), or (iii). In certain embodiments, both R6 and R7 are ndently 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 selected from any one of the amino acid side chain groups listed n.

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

As generally defined 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 a (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 substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted aryl, a nitrogen ting group, or a group of the formula (i), (ii), or (iii); optionally n R3 and an R1 group are joined to form an optionally substituted 5—6 membered heterocyclic ring; In n embodiments, R3 is en. In certain embodiments, R3 is optionally substituted alkyl; e.g., optionally 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, optionally substituted C3_6alkenyl, optionally substituted C4_6alkenyl, optionally substituted C4_5alkenyl, 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 substituted C3_4alkynyl.

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

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

In certain embodiments, R3 is optionally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, R3 is optionally substituted heteroaryl, e.g., optionally substituted 5— l4 membered heteroaryl, ally substituted 5—10 membered heteroaryl, ally 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 embodiments, 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 embodiments, R3 and an nt 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 ments, 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 certain embodiments, both R2 and R3 are independently a group of the formula (i), (ii), or (iii). In certain embodiments, both R2 and R3 are independently a group of the formula (i). In certain ments, both R2 and R3 are independently a group of the formula (ii). In certain embodiments, both R2 and R3 are ndently a group of the formula (iii). In certain embodiments, both R2 and R3 are the same group, selected from a group of the a (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, 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 an sulfur atom, a nitrogen protecting group when ed to a nitrogen atom, or two RA4 groups are joined to form an optionally substituted heterocyclic or optionally substituted heteroaryl ring. 2012/062222 In certain embodiments, R4 is —ORA4, wherein RA4 is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, or an oxygen protecting group. In certain embodiments, RA4 is hydrogen or optionally tuted alkyl. In certain embodiments, RA4 is hydrogen.

In certain embodiments, R4 is —N(RA4)2, wherein each occurrence of RA4 is independently hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted cyclyl, optionally substituted aryl, optionally substituted heteroaryl, 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, at least one instance of RA4 is hydrogen or optionally substituted alkyl. In certain embodiments, at least one instance of RA4 is en.

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

As generally defined 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 Formula (I) are contemplated .

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 thereof. In certain embodiments, at least one R1 is a group of a (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 a (i). In certain 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 ments, R5 is hydrogen. In certain embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In n 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 ments, 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 (i), the compound is of a (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 certain embodiments, R3 is a group of formula (i). In certain embodiments, R3 is a group of formula (ii). In certain ments, 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 certain 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—f2), wherein each instance of R1 is a group of the formula (iv), provided is a compound of Formula (I—f3): (I—f3) or salt thereof. In certain embodiments, L is an ally 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 a (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 en. In certain embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In n embodiments, n is 3. In certain ments, 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 formula (iV), provided is a compound of Formula (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 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 n 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).

In certain embodiments of Formula (I—f), wherein R2 is a group of formula (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 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 ments, R4 is — ORA4. In certain embodiments, R5 is hydrogen. In certain ments, n is 0. In certain embodiments, n is 1. In n 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—f6), wherein each instance of R1 is a group of the formula (iV), ed is a compound of Formula (I—f7): (1-f7 ) 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 embodiments, R6 is a group of a (iii). In certain embodiments, R7 is a group of formula (i). In n 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 ndently 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 WO 63468 embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain ments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

For example, in n embodiments of Formula (I—f8), wherein each instance of R1 is a group of the formula (iV), provided is a nd of Formula (I—f9): (1-f9) or salt thereof. In n 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 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 formula (iii), the compound is of a (I—f10): ” (I—f10) or salt f. In certain ments, 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 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 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—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 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 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 (iii), the compound 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 n 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), n each instance of R1 is a group of the formula (iV), provided is a nd 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 certain embodiments, R6 is a group of formula (ii). In n embodiments, R6 is a group of formula (iii). In certain embodiments, R7 is a group of a (i). In certain ments, R7 is a group of a (ii). In certain embodiments, R7 is a group of formula (iii).

Compounds ofFormula (II) Compounds of a (11) may be prepared Via internal cyclization of the addition t 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' E_B?:'_\l_: RL '____B_iR8’N RL R8’N\H<RL R' R' R' secondary amino group amino substituents imino nitrogens Thus, in a second , provided is a compound of a (II): or salt thereof; wherein: each instance of R’ is independently hydrogen or optionally substituted alkyl; each instance of R1 is ndently en, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted 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, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted aryl, 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 en atom, or two RAl groups are joined to form an optionally substituted heterocyclic or optionally substituted 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, wherein RW is hydrogen, optionally tuted alkyl, optionally substituted l, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, ally 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 substituted alkyl, optionally substituted l, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted 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, n 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; 2012/062222 Y is O, S, NRY, wherein RY is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally 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 tuted 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, 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 specifically ed: 0 o o 0 0 o 0 R60 0 N\)\ ,N\)\ ,N Me/ RL, R8 RL, R8 RL, R8,N\)\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 lly defined above, each instance of R’ is ndently hydrogen or ally substituted alkyl. In certain ments, at least one instance of R’ is hydrogen.

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

As generally defined above, each ce of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, 2012/062222 optionally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally tuted heteroaryl, halogen, —ORA1, —N(RA1)2, or —SRA1.

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

In certain ments, at least one ce 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 optionally substituted C34alkyl.

In certain embodiments, at least one instance of R1 is optionally 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 R1 is optionally substituted alkynyl, e.g., optionally substituted kynyl, optionally substituted C3_6alkynyl, ally substituted C4_6alkynyl, ally 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 substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or optionally tuted C6 carbocyclyl.

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 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 ally substituted aryl, e.g., optionally substituted phenyl.

In certain embodiments, at least one instance of R1 is optionally substituted heteroaryl, e.g., ally tuted 5—14 membered heteroaryl, optionally tuted 5—10 membered heteroaryl, optionally substituted 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 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 instance of R6 and R7 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a en atom, an oxygen ting group when ed 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 tuted with an amino group of the formula (R7). In that ce, 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 substituted alkenylene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, optionally substituted carbocyclylene, optionally tuted heterocyclylene, optionally tuted 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, optionally substituted alkynyl, optionally substituted yclyl, 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): (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 embodiments, at least four instances of R1 is a group of a (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 embodiments, R1 alpha to the group —C(=W)—Y— is a group of formula (iv).

In certain ments, 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 ed 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 formula (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 substituted C4_20alkylene, optionally substituted C6_20alkylene, ally substituted Cg_20alkylene, optionally substituted C10_20alkylene, optionally substituted C1_6alkylene, optionally substituted C2- 6alkylene, optionally substituted C3_6alkylene, optionally tuted C4_6alkylene, optionally substituted C4_5alkylene, or optionally substituted C3_4alkylene.

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

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

In certain embodiments, L is an optionally substituted heteroalkylene; e.g., ally substituted heteroC1_50alkylene, optionally substituted heteroC1_40alkylene, ally substituted heteroC1_30alkylene, optionally substituted heteroC1_20alkylene, optionally substituted C4_20alkylene, optionally substituted heteroC6_20alkylene, optionally substituted heterng_20all<ylene, optionally tuted 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 ments, L is an optionally substituted heteroalkenylene, e.g., optionally substituted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, optionally substituted heteroC2_30alkenylene, optionally substituted heteroC2_20alkenylene, optionally substituted C4_20alkenylene, ally substituted heteroC6_20alkenylene, optionally substituted heterng_20all<enylene, optionally substituted heteroC10_20alkenylene, optionally substituted heteroC2_6alkenylene, optionally substituted C3_6alkenylene, optionally substituted heteroC4_6alkenylene, optionally substituted heteroC4_5alkenylene, or optionally substituted heteroC3_4alkenylene.

In n embodiments, L is an optionally substituted alkynylene, e.g., optionally substituted heteroC2_50alkynylene, optionally substituted heteroC2_40alkynylene, optionally substituted C2_30alkynylene, optionally tuted heteroC2_20alkynylene, optionally substituted heteroC4_20alkynylene, optionally substituted heteroC6_20alkynylene, optionally substituted heterng_20all<ynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, optionally 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 ally substituted C6 carbocyclylene.

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

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

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

For example, in certain embodiments, n L is an optionally substituted 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, ive. In certain embodiments, q is an integer between 1 and 30, inclusive. In certain embodiments, q is an r 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 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 n embodiments, q is 4. In n ments, q is 5. In certain ments, q is 6. In certain embodiments, q is 7. In certain embodiments, q is 8. In certain ments, q is 9. In certain embodiments, q is 10.

In certain embodiments, both R6 and R7 are en. 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 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 n embodiments, both R6 and R7 are independently a group of the formula (ii). In certain embodiments, both R6 and R7 are ndently 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 selected from any one of the amino acid side chain groups listed n.

In certain embodiments, each instance of R1 is the same. In n embodiments, at least one R1 group is different. In n 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, optionally substituted 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, 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, ally tuted aryl, or a nitrogen ting group. In certain embodiments, Y is O. In certain embodiments, each instance of Y is S. In certain embodiments, Yis NRY. In certain embodiments, RY is en or a nitrogen protecting group.

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

As generally defined 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 ce 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 certain embodiments, R8 is a group of the formula (i). In certain embodiments, R8 is a group of the formula (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 ments, 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) 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 a (i), (ii), or (iii). In n 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 nt R1 group are joined to form an ally 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 a (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 nd of Formula (II—a): RS’N\ARL (II—a) or salt f. 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 n 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 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 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 Formula (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): R7—N—LWJKFf o RS’N\ARL (II-b) 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 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 (V), provided is a nd of Formula (II—c): “ (II-c) or salt thereof. In certain embodiments, at least one R1 is a group of formula (iV). In certain embodiments, R2 is a group of a (i). In n embodiments, R2 is a group of formula (ii). In certain embodiments, R2 is a group of formula (iii). In certain ments, 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 n 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 n embodiments, m is 1.

In n embodiments of Formula (II—c), wherein R1 alpha to the group — C(=O)—O— is a group of a (iV), ed is a compound of Formula (II—cl): 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 substituted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of a (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 the formula (i), (ii), or (iii).

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

In certain embodiments of Formula (II—a), wherein R8 is a group of formula (i), provided is a nd of Formula (II—d): R YP /\\/N\)\RL RL (II—d) or salt thereof. In certain 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—d), wherein R1 alpha to the group — C(=O)—O— is a group of formula (iv), provided is a compound of Formula (II—dl): RL (II—d1) or salt thereof. In certain ments, L is an optionally tuted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of a (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 n 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 (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 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 ments of Formula (II—e), n R1 alpha to the group — C(=O)—O— is a group of formula (iv), provided is a nd of Formula (II—el): R6 o R —N—L7 \ARL O (II-el) 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 n embodiments, R7 is a group of formula (iii). In certain embodiments, both R6 and R7 are ndently groups of the a (i), (ii), or (iii).

In certain embodiments of Formula (II—a), wherein R8 is a group of formula (iii), provided is a nd of Formula (II—f): RLVN\ARL (II-f) 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 (II—f), wherein 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 a (i). In certain embodiments, R6 is a group of formula (ii). In certain ments, R6 is a group of formula (iii). In certain ments, 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), wherein R1 and R8 are joined to form an optionally substituted 5—6 membered heterocyclic ring, provided is a compound 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 t of the same or different two, three, four, five, siX, seven, eight, nine, or ten amino acids, and which further comprise one or more sites of conjugation attached thereto, e.g., to an internal amide nitrogen, to an amino substituent, 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 tuents imino nitrogens ] Thus, in a third , ed 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 hydrogen, 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), (iii); each instance of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted l, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally 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 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 RAl groups are joined to form an optionally substituted cyclic or optionally substituted heteroaryl ring; and each instance of R2 is independently hydrogen, optionally substituted alkyl, optionally substituted l, 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); and Formulae (i), (ii), and (iii) are: RLB—YRP H\ RL RI :4 (1) (ii) (iii) wherein: each ce of R’ is independently hydrogen or ally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally tuted carbocyclyl, optionally substituted heterocyclyl, ally 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 substituted heterocyclyl, ally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is hydrogen, optionally substituted alkyl, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted yclyl, 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 tuted C250 alkenyl, optionally substituted C250 alkynyl, ally substituted heteroC1_50 alkyl, optionally substituted heteroC2_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, p is an integer of between 1 and 9, inclusive. In certain embodiments, p is 1. In certain ments, p is 2. In certain embodiments, p is 3. In certain embodiments, p is 4. In certain ments, p is 5. In certain embodiments, p is 6.

In certain embodiments, p is 7. In certain embodiments, p is 8. In n embodiments, 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 Formula (III—b): RRZ/Nfi Q (III-b) or salt f.

In n embodiments, wherein p is 3, the compound of Formula (III) is a compound of Formula (III—c): R2 R1 (III-c) 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 ments, 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 R2\N:\l:oN\R2 R2 Rz,N QA/Nfiw R1 0 ) or salt thereof.

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

In certain embodiments, wherein p is 7, the compound of a (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 nd of Formula (111) is a compound of Formula (III—h): R1 R2 (III—h) or salt thereof. 2012/062222 ] In certain embodiments, wherein p is 9, the compound of Formula (III) is a compound of a (III—i): QR1RZQR1 RVfNJYlfideJYQ or salt thereof.

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 ments, 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 substituted alkyl, e.g., . In certain embodiments, one instance of R’ is optionally substituted alkyl, and the rest are hydrogen.

As generally defined above, each ce of Q is independently O, S, or NRQ, wherein RQ is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted l, optionally substituted carbocyclyl, ally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group, or a group of the formula (i), (ii), or (iii). In certain ments, at least one instance of Q is O. In n 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 tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted 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, ally substituted C2_6alkyl, optionally tuted C3_6alkyl, optionally substituted C4_6alkyl, optionally substituted C4_5alkyl, or optionally substituted C34alkyl.

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

In certain ments, 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 membered heterocyclyl, ally substituted 5—6 membered heterocyclyl, optionally substituted 5 membered heterocyclyl, or optionally substituted 6 ed 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 tuted 5—10 membered heteroaryl, optionally substituted 5—6 ed heteroaryl, optionally substituted membered heteroaryl, or optionally substituted 6 membered heteroaryl.

In any of the above embodiments, the R1 alkyl, alkenyl, alkynyl, carbocyclyl, cyclyl, aryl, or heteroaryl group may be tuted, for example, with an optionally substituted amino group (e.g., ), an optionally tuted hydroxyl group (e.g., —OR6), an ally 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, ally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally 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).

For example, in certain embodiments, at least one ce of R1 is an alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl group tuted 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 tuted alkenylene, optionally substituted alkynylene, optionally substituted heteroalkylene, optionally substituted heteroalkenylene, optionally substituted heteroalkynylene, ally substituted carbocyclylene, optionally substituted heterocyclylene, optionally substituted arylene, or ally 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 tuted 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): 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 instances 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 embodiments, at least four instances of R1 is a group of formula (iv). In certain embodiments, at least five ces of R1 is a group of formula (iv). In certain embodiments, at least six instances of R1 is a group of a (iv). In certain embodiments, at least seven ces of R1 is a group of formula (iv). In certain embodiments, at least eight instances of R1 is a group 2012/062222 of formula (iV). In certain 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 ments, L is an optionally substituted alkylene; e.g., optionally substituted C1_50alkylene, optionally substituted C1_40alkylene, optionally tuted C1- lene, optionally substituted lkylene, 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, optionally substituted C4_6alkylene, optionally substituted C4_5alkylene, or optionally substituted C3_4alkylene.

] In certain embodiments, L is an optionally substituted lene, e.g., optionally substituted C2_50alkenylene, optionally substituted C2_40alkenylene, optionally substituted C2_30alkenylene, optionally substituted Cnoalkenylene, optionally substituted C4- nylene, optionally substituted lkenylene, optionally substituted Cg_20all<enylene, optionally substituted C10_20alkenylene, optionally substituted kenylene, optionally substituted C3_6alkenylene, optionally substituted C4_6alkenylene, optionally substituted C4- 5alkenylene, or optionally substituted C3_4alkenylene.

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

In certain embodiments, L is an optionally substituted heteroalkylene; e.g., optionally substituted heteroC1_50alkylene, optionally substituted heteroC1_40alkylene, optionally substituted C1_30alkylene, optionally substituted heteroC1_20alkylene, optionally substituted C4_20alkylene, optionally substituted heteroC6_20alkylene, optionally substituted heterng_20all<ylene, optionally substituted heteroC10_20alkylene, optionally tuted C1_6alkylene, optionally substituted heteroC2_6alkylene, optionally substituted heteroC3_6alkylene, optionally substituted heteroC4_6alkylene, optionally substituted heteroC4_5alkylene, or ally substituted heteroC3_4alkylene.

In n embodiments, L is an optionally substituted heteroalkenylene, e.g., optionally tuted heteroC2_50alkenylene, optionally substituted heteroC2_40alkenylene, optionally substituted heteroC2_30alkenylene, optionally substituted heteroC2_20alkenylene, optionally substituted heteroC4_20alkenylene, optionally substituted heteroC6_20alkenylene, optionally substituted g_20all<enylene, optionally substituted heteroC10_20alkenylene, optionally substituted heteroC2_6alkenylene, optionally substituted heteroC3_6alkenylene, optionally tuted heteroC4_6alkenylene, ally substituted C4_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, optionally tuted heteroC2_30alkynylene, optionally substituted heteroC2_20all<ynylene, optionally substituted heteroC4_20alkynylene, optionally substituted heteroC6_20alkynylene, optionally substituted heterng_20all<ynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, optionally substituted heteroC3_6alkynylene, optionally substituted heteroC4_6alkynylene, optionally substituted heteroC4_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 yclylene, 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, ally substituted 5—8 membered heterocyclylene, optionally substituted —6 membered heterocyclylene, optionally substituted 5 membered heterocyclylene, or ally substituted 6 membered heterocyclylene.

In certain ments, 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 heteroarylene, ally substituted 5—6 membered heteroarylene, optionally substituted 5 membered heteroarylene, or optionally tuted 6 membered heteroarylene.

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

In n 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 r between 1 and 20, inclusive. In certain embodiments, q is an integer n 4 and , inclusive. In certain embodiments, q is an integer between 6 and 20, inclusive. In certain embodiments, q is an integer n 8 and 20, inclusive. In n embodiments, q is 1. In n 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 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 formula (ii). In certain embodiments, R6 is hydrogen and R7 is a group of the a (iii). In certain embodiments, both R6 and R7 are independently a group of the formula (i), (ii), or (iii). In certain ments, 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 tood 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.

As generally d above, each instance of R2 is independently hydrogen, ally 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): . Fa' )(FRL H; o R, 01' §_/RL (i) (ii) (iii) wherein R’, X, Y, RL, and RP are as defined herein.

In certain ments, at least one ce of R2 is optionally substituted alkyl; e.g., optionally substituted C1_6alkyl, optionally substituted C2_6alkyl, optionally substituted kyl, optionally substituted C4_6alkyl, optionally substituted C4_5alkyl, or ally substituted C34alkyl.

In certain embodiments, at least one instance of R2 is optionally substituted alkenyl, e.g., optionally substituted kenyl, optionally substituted kenyl, optionally substituted C4_6alkenyl, optionally substituted C4_5alkenyl, or optionally substituted C3- 4alkenyl.

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

In certain embodiments, at least one instance of R2 is optionally substituted carbocyclyl, 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 membered heterocyclyl, optionally substituted 3—10 ed 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 membered heteroaryl, optionally substituted 5—10 membered heteroaryl, optionally substituted 5—6 membered heteroaryl, optionally tuted ed heteroaryl, or ally substituted 6 membered heteroaryl.

In certain embodiments, at least one instance of R2 is a nitrogen ting 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 ments, 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 a (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 n 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 formula (i), (ii), or (iii). s combinations of the above embodiments of Formula (III) are contemplated .

] For example, in certain ments, wherein each instance of Q is O, the compound of Formula (III) is a compound of Formula (III—a): p (III-a) 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 n 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 n 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 instance of R1 is a group of formula (iv). In certain embodiments, R2 is hydrogen. 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 n 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 tuted alkylene. In certain embodiments, R6 is a group of formula (i). In certain embodiments, R6 is a group of formula (ii). In n 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 a (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

In certain embodiments of Formula (III—a), wherein each instance of R1 is a group the formula (iV), provided is a compound of Formula ): (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 certain embodiments, at least one instance of R2 is a group of formula (iii). In certain ments, 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 n 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 n embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

In certain embodiments of Formula (III—c), wherein p is 1, provided is a compound of Formula (III—cl): Riff/R7 R7 (III-cl) or salt f. 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 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 ments, 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 ments of Formula (III—cl), wherein each instance of R2 is hydrogen, 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 ments, L is an optionally substituted alkylene. In certain ments, 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 ments, R7 is a group of formula (i). In n ments, 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 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 3): R6\N,R7 o o R\6 NH IN q R7 (III-c3) or salt thereof, wherein q is an integer between 1 and 10, inclusive. 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 WO 63468 (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 (III—a), wherein 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 (III—d): p (III-d) or salt thereof. In certain embodiments, at least one R1 is a group of a (iv). In certain embodiments, each instance of R1 is a group of formula (iv). In certain embodiments, each instance of R2 is en. 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 n 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 n embodiments of Formula (III—a), n at least one instance of R2 is a group of formula (ii) and each instance of R’ is hydrogen, provided is a compound of Formula (III—e): p (III-e) or salt thereof. In certain ments, 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 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 ments, p is 2. In certain embodiments, p is 3.

In certain embodiments of Formula (III—a), n at least one ce of R2 is a group of formula (iii), ed 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 formula (iv). In n 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 ments, p is 3.

Compounds ofFormula (IV), (V), and (V1) Compounds of Formula (IV), (V), and (VI), while not ucted 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 present 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 a (IV), (V), or Q} R1jgi§1§£§ (V1) or salt thereof; each instance of Q is independently O, S, or NRQ, wherein RQ 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 formula (i), (ii), (iii); each instance of R1 is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally 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, 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 an sulfur atom, a en protecting group when attached to a nitrogen atom, or two RAl groups are joined to form an optionally tuted heterocyclic or optionally substituted heteroaryl ring; each instance of R2 is independently hydrogen, ally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally substituted carbocyclyl, optionally tuted 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 optionally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, optionally substituted alkyl, optionally tuted alkenyl, ally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; Y is O, S, NRY, wherein RY is hydrogen, optionally substituted alkyl, ally substituted alkenyl, ally 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 yclyl, optionally substituted heterocyclyl, optionally tuted 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 en atom; and RL is optionally substituted C150 alkyl, ally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted heteroC1_50 alkyl, optionally tuted heteroC2_50 alkenyl, ally 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, optionally tuted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally tuted 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 instance of Q is O. In certain embodiments, at least one instance of Q is S. In certain ments, each instance of Q is S. In certain embodiments, at least one instance of Q is NRZ. In certain ments, each instance of Q is NRZ. In certain embodiments, each ce 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 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 ally substituted 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 substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted yclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted heteroaryl, n, —ORA1, —N(RA1)2, or —SRA1.

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

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

In certain embodiments, at least one instance of R1 is ally substituted alkenyl, e.g., optionally tuted 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 R1 is optionally substituted alkynyl, e.g., optionally substituted kynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted kynyl, 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 substituted C5_g carbocyclyl, optionally substituted C5_6 carbocyclyl, optionally substituted C5 carbocyclyl, or ally substituted C6 carbocyclyl.

] 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 membered heterocyclyl, ally substituted 5—6 ed 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 tuted phenyl.

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

In any of the above embodiments, the R1 alkyl, l, 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), n each instance of R6 and R7 is independently hydrogen, optionally substituted alkyl, WO 63468 optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, ally 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 ed 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, 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 alkenylene, ally 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 ting of hydrogen, optionally substituted alkyl, optionally substituted 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): 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 ne; 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, ally substituted Cg_20all<ylene, optionally substituted C10_20alkylene, ally substituted C1_6alkylene, optionally substituted C2- 6alkylene, optionally substituted C3_6alkylene, optionally substituted C4_6alkylene, optionally tuted C4_5alkylene, or ally 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, ally substituted C2_20alkenylene, optionally substituted C4- goalkenylene, optionally substituted C6_20alkenylene, optionally substituted Cg_20all<enylene, optionally substituted C10_20alkenylene, optionally substituted kenylene, optionally substituted C3_6alkenylene, optionally substituted C4_6alkenylene, optionally substituted C4- 5alkenylene, or optionally substituted kenylene.

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

In n embodiments, L is an optionally substituted alkylene; e.g., optionally substituted heteroC1_50alkylene, optionally substituted C1_40alkylene, optionally substituted C1_30alkylene, optionally substituted heteroC1_20alkylene, optionally substituted heteroC4_20alkylene, optionally substituted heteroC6_20alkylene, optionally substituted heterng_20all<ylene, optionally substituted heteroC10_20alkylene, optionally tuted heteroC1_6alkylene, optionally substituted heteroC2_6alkylene, optionally substituted heteroC3_6alkylene, optionally substituted heteroC4_6alkylene, ally 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 tuted heteroC2_30alkenylene, optionally substituted heteroC2_20all<enylene, optionally substituted C4_20alkenylene, optionally tuted heteroC6_20alkenylene, optionally substituted heterng_20alkenylene, optionally substituted heteroC10_20alkenylene, optionally tuted 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 heteroalkynylene, 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 substituted g_20all<ynylene, optionally substituted heteroC10_20alkynylene, optionally substituted heteroC2_6alkynylene, optionally substituted C3_6alkynylene, optionally substituted heteroC4_6alkynylene, optionally substituted heteroC4_5alkynylene, or optionally substituted heteroC3_4alkynylene.

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

In certain embodiments, L is an optionally substituted heterocyclylene, e.g., ally substituted 3— l4 membered cyclylene, optionally substituted 3—10 membered 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 arylene, 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 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 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 n 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 ments, q is an integer between 6 and 20, inclusive. In certain embodiments, 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 embodiments, q is 5. In certain embodiments, q is 6. In certain embodiments, q is 7. In certain embodiments, q is 8. In certain ments, 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 formula (ii). In certain ments, 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 formula (i), (ii), or (iii). In n 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 ments, 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 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 embodiments, 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, ally substituted alkenyl, optionally substituted l, 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): 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 tuted C1_6alkyl, optionally substituted C2_6alkyl, ally substituted C3_6alkyl, optionally substituted C4_6alkyl, optionally substituted C4_5alkyl, or ally substituted C34alkyl.

In certain embodiments, at least one ce of R2 is optionally substituted 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 R2 is optionally tuted alkynyl, e.g., optionally tuted C2_6alkynyl, optionally substituted C3_6alkynyl, optionally substituted C4_6alkynyl, optionally substituted C4_5alkynyl, or ally 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., ally substituted 3—14 membered cyclyl, optionally substituted 3—10 ed 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 R2 is optionally substituted aryl, e.g., ally substituted phenyl.

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

In n 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 ments, 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 ce, 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 formula (i), (ii), or (iii).

Various combinations 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 a (IV), (V), or (VI) is a compound of Formula (IV—a), (V—a), or {i} 1:1i1fii1 R(—IVa)0 (V—a)0 0(—VIa)R or salt thereof. In certain embodiments, at least one instance of R1 is a group of formula (iv).

In n embodiments, each instance of R1 is a group of formula (iv). In certain embodiments, at least one ce of R2 is optionally substituted alkyl, optionally substituted alkenyl, or ally tuted 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 : 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 tuted alkynyl. In certain embodiments, at least one instance of R2 is a group of formula (i). In n 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 ments, 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 a (iii). In certain embodiments, both R6 and R7 are independently groups of formula (i), (ii), or (iii).

WO 63468 In certain embodiments of Formula (IV—b), (V—b), or (VI—b), wherein both R1 groups are a group the formula (iv), ed is a compound of Formula (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 embodiments, at least one instance of R2 is optionally substituted alkyl, optionally tuted 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 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 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 , wherein at least one instance of R2 is a group of formula (i) and each instance of R’ is hydrogen, provided is a compound of ae (IV—d), (V—d), and : @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 instance of R1 is a group of a (iv).

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

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

In certain ments of Formulae (IV—a), (V—a), and (VI—a), wherein at least one instance of R2 is a group of formula (ii) and each instance of R’ is hydrogen, provided is a compound of Formulae (I\72—f), (V—f), and (VI—f): :?“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 n 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 ae , (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 nd of Formulae (IV—g), (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 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 a (iv).

In certain ments of Formulae (IV—a), (V—a), and , wherein at least one instance of R2 is a group of formula (iii), provided is a nd 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 ce of R1 is a group of formula (iv). In certain embodiments, R2 is optionally substituted alkyl, optionally substituted alkenyl, or optionally tuted 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 are a group of formula (iii), provided is a compound 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 sion, 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 independently hydrogen or optionally substituted alkyl; X is O, S, NRX, wherein RX is hydrogen, ally substituted alkyl, optionally substituted l, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted 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 tuted alkenyl, optionally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, or a nitrogen protecting group; RP is en, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally tuted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, an oxygen protecting group when ed 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 C1_50 alkyl, optionally substituted heteroC2_50 alkenyl, ally substituted heteroC2_50 alkynyl, or a polymer.

In the case of Formula (II), the at least one instance of group of formula (i) is orated 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, ally substituted l, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally tuted aryl, optionally substituted heteroaryl, or a nitrogen ting group. In certain embodiments of formula (i), Y is NRY, wherein 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 tood that RL may be substituted at either carbon. Nucleophilic attack of an amino or amide group at the least sterically hindered carbon of the e, 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 e, thiirane, or aziridine of formula (i—X) provides a group of the formula (i—bl), (i—b2), or (i—b3) (route b), n RP is hydrogen (Scheme 6). It is understood that compounds of the present invention may comprise a e 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 depicted in the Formulae seeks to encompasses all contemplated modes of on.

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 tuted group, wherein RP is a group other than hydrogen, i.e., wherein RP is independently selected from 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 a sulfur atom, or a nitrogen protecting group when attached to a nitrogen atom; using conventional methods. tion, acylation, and/or protection of a yl, 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 Methods of Organic Synthesis, 3rd n, Cambridge University Press, Cambridge, 1987.

For example, in certain non—limiting embodiments, the hydroxyl, 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 formula (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 substituted alkynyl. In certain embodiments of formula (i), RP is optionally substituted carbocyclyl. In n ments of formula (i), RP is optionally tuted heterocyclyl.

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

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

It is understood from the present disclosure that the group of a (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 provides a mixture of APPLs comprising more APPLs conjugated to a group of a (i—a) than formula (i—b), e.g., 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%, n 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 ed to formula (i—a).

In certain embodiments, the epoxide, thiirane, or ine of formula (i—x) is , i.e., having (R) or (S) stereochemistry. Chiral epoxides, thiiranes, and aziridines can be obtained from a variety of sources which are familiar to those skilled in the art of organic synthesis. In some embodiments, the chiral e, thiirane, or aziridine is obtained cially. In some embodiments, the chiral epoxide, thiirane, or aziridine is synthesized according to s known to those of skill in the art, such as, but not limited to the Sharpless epoxidation of primary 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 ; Vol. 63, p.66 (1985); Katsuki 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., racemic 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 nd containing a heavy atom attached thereto, obtaining the optical rotation of the nd, and/or NMR analysis after chemical modification of the optically active compound with a chiral derivatizing agent are some methods useful in evaluating chirality.

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 ments, wherein the epoxide, thiirane, or aziridine of formula (i—x1) is chiral, the conjugation reaction is elective, and the reaction provides a chiral mixture of APPLs comprising more APPLs conjugated to a group of formula (i—a1) than formula (i—b1), 6.57., the on mixture comprises greater than 50%, r 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 ine of formula (i— x2) is chiral, the conjugation reaction is regioselective, and the reaction es a chiral mixture of APPLs comprising more APPLs conjugated to a group of formula (i—a2) than formula (i—b2), 6.57., the reaction mixture comprises 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 ed to formula (i—a2).

In certain embodiments, an APPL, and in ular, a compound of Formulae (I), (II), (III), (IV), (V), or (VI), comprises at least one instance of a group of the formula (ii) ed 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, n RX is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, ally substituted heteroaryl, or a nitrogen protecting group. In certain embodiments of formula (ii), X is NRX, wherein RX is hydrogen, optionally tuted 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: 2012/062222 (iii).

As generally defined above, RL is optionally substituted C150 alkyl, ally substituted C250 alkenyl, optionally substituted C250 alkynyl, optionally substituted C150 heteroalkyl, ally substituted C250 heteroalkenyl, optionally substituted C250 heteroalkynyl, or a polymer. The group RL seeks to encompass lipophilic, hydrophobic, and/or non—polar , 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 embodiments, RL is an ally tuted C6_40alkyl. In certain embodiments, RL is an ally substituted C6_30alkyl. In certain embodiments, RL is an optionally substituted C6- goalkyl. In certain embodiments, RL is an optionally substituted Cg_20alkyl. In certain embodiments, RL is an optionally substituted Cgalkyl. In certain embodiments, RL is an optionally substituted 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 tuted Clgalkyl. In certain embodiments, 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 certain ments, RL is an optionally tuted yl. 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 tuted C19alkyl. In certain embodiments, RL is an optionally substituted Czoalkyl. In any of the above embodiments, the group RL is an unsubstituted alkyl group.

In n 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, -C7H15, -C8H17, -C9H19, -C10H21, -C11H23, -C12H25,-C13H27, -C14H29, - C15H31, -C16H33, -C17H35, -C18H37, -C19H39, -C20H41, -C21H43, -C22H45, 7, -C24H49, and -C25H51- In certain embodiments, at least one instance of RL is a substituted alkyl. For example, in n menets, at least one instance of RL is an alkyl substituted with one or more fluorine substituents. Exemplary fluorinated alkyl groups include, 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 FFFFFFFFFFF FFFFFF Fr" F FFFFFFFFFFFFFFF FFFFFFFF FFFFFFFFFF F FFFFF WF s" F FFFFFFFFFFFFFFFF FFFFFFFFFrrrr FFFFFFFFFFFFFFFFF FFFFFFFF x F FFFFFFFFFFFFFFFF FFFFFFFFFF FFFFFFFFFFFFFFFFFF 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 lkenyl. In certain embodiments, RL is an optionally substituted lkenyl. In certain embodiments, RL is an ally substituted C6_20alkenyl. In certain embodiments, RL is an optionally substituted Cg_20alkenyl.

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

In n embodiments, RL is an optionally substituted Clzalkenyl. In certain ments, RL is an optionally substituted C13alkenyl. In certain embodiments, RL is an optionally substituted C14alkenyl. In certain embodiments, RL is an optionally substituted enyl.

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

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

] Exemplary unsubstituted alkenyl groups e, but are not limited to: /\”H W My“, N63: Wt“: /\/\/\/\/\/\/\/\r‘yv W\/\/\/\/\/\/\\ arr W\ Jr, g oleic —(CH2)7CH=CH(CH2)3CH3, Palmitoliec —(CH2)7CH=CH(CH2)5CH3, Sapienic —(CH2)4CH=CH(CH2)3CH3, Oleic —(CH2)7CH=CH(CH2)7CH3, Linoleic 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 groups, such groups are meant to encompass lipophilic groups (also referred to as a “lipid tail”). ilic 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 saturated and unsaturated, depending on whether or not the lipid tail comprises double bonds. The lipid tail can also comprise 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 greater than 12 carbons and up to 22 carbons, e.g., C1342 alkyl or C1342 l), or very long (i.e., with tails greater than 22 carbons, e.g., C2330 alkyl or C2330 alkenyl).

In certain embodiments, RL is an optionally tuted C250 l. In certain embodiments, RL is an ally substituted C6_50alkynyl. In certain ments, RL is an optionally substituted C640alkynyl. In certain embodiments, RL is an optionally substituted C6_30alkynyl. In certain embodiments, RL is an optionally substituted C6_20alkynyl. In certain embodiments, RL is an optionally substituted Cg_20all<ynyl. In certain embodiments, RL is an optionally substituted Cgalkynyl. In certain embodiments, RL is an optionally substituted Cgalkynyl. In certain embodiments, RL is an optionally substituted Cloalkynyl. In certain embodiments, RL is an optionally substituted C11alkynyl. In certain embodiments, RL is an optionally substituted Clzalkynyl. In certain embodiments, RL is an optionally tuted C13alkynyl. In n embodiments, RL is an optionally substituted ynyl. 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 ments, RL is an optionally substituted Clgalkynyl. In certain ments, RL is an optionally substituted Clgalkynyl. In certain embodiments, RL is an optionally substituted Czoalkynyl. In any of the above embodiments, the group RL is an unsubstituted alkynyl group.

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

In n 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 C6_20alkyl. In certain ments, 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 embodiments, RL is an optionally substituted heteroC11alkyl. In certain embodiments, RL is an optionally substituted heteroClzalkyl. In certain embodiments, RL is an optionally substituted heteroC13alkyl. In certain ments, RL is an optionally substituted heteroC14alkyl. In certain embodiments, RL is an optionally substituted heteroC15alkyl. In certain embodiments, RL is an optionally substituted heteroC16alkyl. In certain ments, 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 tituted heteroalkyl 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: WOA‘J": WOAHH /\/\/\/\/\/\/\/\ /\O O/\IJJJ r51 In certain embodiments, at least one instance of RL is an optionally tuted heteroC2_50alkenyl. In certain embodiments, RL is an optionally substituted heteroC6_ 50alkenyl. In certain embodiments, RL is an optionally substituted heteroC6_40alkenyl. In n embodiments, RL is an optionally substituted heteroC6_30alkenyl. In certain embodiments, RL is an ally 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 galkenyl. In certain embodiments, RL is an optionally substituted Cloalkenyl.

In certain embodiments, RL is an optionally substituted heteroC11alkenyl. In certain embodiments, RL is an optionally substituted heteroClzalkenyl. In n embodiments, RL is an ally tuted heteroC13alkenyl. In certain embodiments, RL is an optionally substituted heteroC14alkenyl. In certain embodiments, RL is an optionally substituted C15alkenyl. In certain embodiments, RL is an ally substituted heteroC16alkenyl.

In certain embodiments, RL is an optionally substituted heteroC17alkenyl. In certain embodiments, RL is an optionally substituted heteroClgalkenyl. In certain embodiments, RL is an ally substituted heteroC19alkenyl. In certain embodiments, RL is an optionally 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 ally substituted heteroC6_40alkynyl. In certain embodiments, RL 2012/062222 is an optionally substituted heteroC6_30alkynyl. In certain embodiments, RL is an optionally substituted heteroC6_20alkynyl. In certain embodiments, RL is an optionally substituted heterng_20alkynyl. In n ments, 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 ments, RL is an optionally substituted heteroC11alkynyl. In certain embodiments, RL is an optionally tuted heteroClgalkynyl. In certain embodiments, RL is an optionally tuted heteroC13alkynyl. In certain embodiments, RL is an optionally substituted heteroC14alkynyl.

In certain embodiments, RL is an optionally substituted heteroC15alkynyl. In n embodiments, RL is an optionally substituted heteroC16alkynyl. In certain ments, RL is an optionally tuted heteroC17alkynyl. In certain embodiments, RL is an optionally substituted heteroClgalkynyl. In certain embodiments, RL is an optionally tuted heteroClgalkynyl. In certain embodiments, RL is an optionally substituted heteroCzoalkynyl.

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 er” 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 biocompatible (i. 6., non—toxic). Exemplary polymers include, but are not limited to, cellulose polymers (e.g., hydroxyethylcellulose, ethylcellulose, ymethylcellulose, methylc cellulose, hydroxypropylmethylcellulose ), dextran polymers, polymaleic 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 present 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) 2012/062222 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 between about 100 to about 200 OC, ive, 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 ts of formula (ii—x) to provide the desired APPL.

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

In another aspect, ed 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 e the d APPL. In certain embodiments, the temperature of the reaction mixture is room temperature e.

In certain embodiments, wherein only one conjugating reagent is used, each instance of RL is the same in the APPL. For example, in n 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 certain embodiments, each instance of RL is the same wherein RL is selected from the group consisting of —CH3, — C2H5, -C3H7, -C4H9, -C5H11, , -C7H15, , -C9H19, -C10H21, -C11H23, -C12H25, - C13H27, -C14H29, -C15H31, -C16H33, -C17H35, -C18H37, -C19H39, and -C20H41- In certain embodiments, each instance of RL is the same wherein RL is an n—alkyl group selected from — CsH17, -C9H19, -C10H21, -C11H23, -C12H25,-C13H27, -C14H29, -C15H31, and -C16H33- atively, 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 reagents), 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) ed thereto.

For example, in certain embodiments, two different epoxides are used in the conjugation reaction. In this instance, in certain embodiments, the APPL comprises two ent RL groups. For example, in n embodiments, the APPL ses a mixture of two different RL groups, wherein the first RL group is an ally 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, tration, 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, llization, chromatography, distillation, etc.

] In n embodiments, the APPL is isolated as a salt. For example, in certain embodiments, the APPL is reacted with an acid (e. 57., an organic acid or inorganic acid) to form the corresponding 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 ting agent, for example, alkyl halides 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 prepared by the ive methods. For example, in certain embodiments, 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. These APPLs may be prepared and/or screened using high—throughput techniques involving liquid handlers, robots, microtiter plates, computers, etc. In certain embodiments, the APPLs are screened for their ability to ect polynucleotides or other agents (e. 57., proteins, peptides, small molecules) into the cell. For example, in one embodiment, provided is a method of screening a compound library, the method comprising providing a plurality of two or more different APPLs and ing the compound library for a d ty.

In one embodiment, a library of different APPLs is ed 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 mixtures 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 ques to identify APPLs with a desired property, e. g. wherein the desired property is solubility in water, solubility at different pH, y to bind polynucleotides, ability to bind heparin, y to bind small molecules, ability to bind protein, ability to form microparticles, ability to increase ction efficiency, y to support cell growth, ability to support cell attachment, ability to support tissue growth, and/or ellular delivery of the APPL and/or an agent complexed or attached thereto to aid in bioprocessing, e. g., for the purpose of manufacturing ns. In certain embodiments the APPLs may be screened for properties or characteristics useful as coatings, additives, materials, and excipients in biotechnology and biomedical applications such as the coating of medical devices or implants with films or multilayer films, as non—biofouling agents, micropatterning agents, and cellular encapsulation agents. In certain embodiments the APPL may be screened for properties or teristics useful in gene therapy (e.g. , the ability 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., polynucleotide, small molecule, antigen, drug, protein, peptide, etc.) to a subject, , organ, or cell.

Exemplary Compounds ofthe Present Invention Certain nds of the present invention are specifically contemplated . For example, compounds comprising tituted n—alkyl RL groups containing 8, 9, , ll, 12, 13, and 14 carbon atoms are ically contemplated. In certain embodiments R1 of such compounds 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 HOC9H19R ORA4 ORA4 HO \C8H17 HO \C9H19 9 9 1 1 HOC10H21 R HO\—C11H23 R ORA4 ORA4 HO \C10H21 HO \OC11H23 9 9 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 C9H19_O o O , , O O C10H21—O/<fi R 1 O R 1 O H H N 3—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 ”/<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 C8H17/\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 /\ N N ORA4 N ORA4 C12H25J n R 1 C13H27J n R 1 O O , , R1 o C14"‘29/\ 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 C12H25, , 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 /wk wk N C12H25 HO/\/\/ C13H27 HO/\/\/ C14H29 C12Hz5 C13Hz7 and C14"‘29 , , , and salts thereof.

Exemplary cyclic dipeptide and cyclic polypeptide 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 and, in particular, —KK and polycyclic lysine APPLs of the formula: CsH17\ WO 63468 WO 63468 CgH1g—O 2012/062222 C11H23—O C12"‘25“O C14H29_O 2012/062222 CBH17_NH CsH17 H O C9H19_N CgH19‘NH CQH’IQ C10H21_NH ‘NH O O HN\ HN\ C10H21 C11H23 H O H O C H —N C12H25—N 13 27 O O C12H25‘NH C13H27—NH 2012/062222 C10H21 C10H21 /_ /_ C13H27 > C14H29 > C13Hz7 and C14H29 and salts thereof.

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

For example, in certain embodiments, ed is a composition comprising an APPL, or salt thereof, and an excipient, wherein the APPL is an amino acid, a linear or cyclic e, 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 ed to an amino group present on the APPL scaffold.

] Compositions, as described herein, comprising an APPL and an excipient of some sort may be useful in a variety of medical and non—medical applications. For example, pharmaceutical compositions sing an APPL and an excipient 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 f.

Cosmetic compositions comprising an APPL and an excipient may be formulated 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 e, etc. Compositions comprising an APPL and an excipient may be useful for non—medical applications, e.g., such as an emulsion or emulsifier, useful, for example, as a food ent, 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 s which incorporate peptide moieties. Thus, compositions comprising an APPL and an excipient may further be useful in cessing, such as a cell’s bioprocessing of a commercially useful chemical or fuel. For example, intracellular delivery of the APPL or an agent complexed thereto 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 example, in certain embodiments, the agent is a small molecule, organometallic compound, nucleic acid, n, peptide, polynucleotide, metal, targeting agent, an isotopically d chemical compound, 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 n 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 covalently 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 n embodiments, the one or more APPLs are in the form of liposomes or micelles. It is understood that, in certain embodiments, these APPLs ssemble 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 liposome may be in the form of a gas, liquid, or solid. The APPLs may be combined with polymers etic or natural), tants, cholesterol, ydrates, proteins, lipids etc. to form the les. These particles may be further combined with an ent to form the ition.

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

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

Exemplary excipients include, but are not limited to, any non—toxic, inert solid, semi—solid or liquid filler, diluent, 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 ; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose, and cellulose acetate; powdered tragacanth; malt; gelatin; talc; ents such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower 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 solution; ethyl alcohol; and phosphate buffer solutions, as well as other non—toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and idants can also be present in the composition, according to the judgment of the formulator. As would be appreciated by one of skill in this art, the excipients may be chosen based on what the ition 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, nts, or drops), bucally, or as an oral or nasal spray. ary 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.

Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose and wood products, natural , cation—exchange resins, calcium ate, silicates, sodium carbonate, cross—linked inyl—pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross—linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline , water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum te (Veegum), sodium lauryl sulfate, quaternary um compounds, etc, and combinations thereof.

Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g. acacia, agar, alginic acid, sodium te, anth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, terol, wax, and lecithin), dal 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 propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl r), carrageenan, cellulosic derivatives (e.g. carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, ypropyl cellulose, hydroxypropyl methylcellulose, cellulose), sorbitan fatty acid esters (e.g. polyoxyethylene sorbitan monolaurate [Tween 20], polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan monooleate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan monostearate [Span 60], sorbitan tristearate [Span 65], glyceryl monooleate, an monooleate [Span 80]), polyoxyethylene esters (e.g. polyoxyethylene earate [Myrj 45], polyoxyethylene hydrogenated castor oil, hoxylated castor oil, polyoxymethylene stearate, and Solutol), e 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 e, ic F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate 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. acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl—pyrrolidone), magnesium aluminum silicate m), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, nic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, eta, and/or combinations thereof.

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

Exemplary antioxidants include alpha tocopherol, ascorbic acid, l palmitate, butylated yanisole, ted hydroxytoluene, monothioglycerol, potassium sulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.

Exemplary chelating agents e ethylenediaminetetraacetic acid (EDTA) and salts and hydrates 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 es thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives e benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, mercuric nitrate, propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, ybenzoic acid, potassium benzoate, ium sorbate, sodium benzoate, sodium propionate, and sorbic acid.

Exemplary alcohol preservatives e ethanol, polyethylene , phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and ethyl alcohol.

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

Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl e (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, paraben, l llS, Germaben II, Neolone, Kathon, and Euxyl. In certain 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, m chloride, calcium citrate, calcium nate, calcium gluceptate, calcium gluconate, D— gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium e, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic ium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, 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 te, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, etc, and combinations f.

Exemplary natural oils include almond, t kernel, avocado, babassu, bergamot, black current seed, , cade, camomile, canola, caraway, a, castor, cinnamon, cocoa butter, t, cod liver, , corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, in, er, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, er, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, , and wheat germ oils. ary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl te, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and combinations thereof.

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

Additionally, the ition 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), hydroxypropyl cellulose (HPC), hydroxypropyl methyl cellulose , hydroxyethylcellulose (MHEC), methylhydroxypropylcellulose (MHPC), ymethyl 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 polysaccharides and polysaccharide derivatives such as starch, dextran, dextran derivatives, chitosan, and alginic acid and its various salts, carageenan, varoius gums, ing xanthan gum, guar gum, gum arabic, gum karaya, gum ghatti, konjac and gum tragacanth, glycosaminoglycans and proteoglycans such as hyaluronic acid and its salts, proteins such as gelatin, collagen, albumin, and fibrin, other polymers, for example, droxyacids such as polylactide, polyglycolide, lactide—co—glycolide) and poly(.epsilon.—caprolactone—co—glycolide)—, carboxyvinyl 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 oxide), and a Pluronic polymer, polyoxyethylene thylene glycol), polyanhydrides, polyvinylalchol, hyleneamine and polypyrridine, polyethylene glycol (PEG) polymers, such as PEGylated lipids 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 l,2—Distearoyl—sn— o—3—Phosphoethanolamine—N—[Methoxy(Polyethylene glycol)—5000]), copolymers and salts thereof.

Additionally, the composition may further comprise an emulsifying agent.

Exemplary emulsifying agents e, but are not limited to, a polyethylene glycol (PEG), a polypropylene glycol, a polyvinyl l, a poly—N—vinyl pyrrolidone and copolymers thereof, poloxamer nonionic surfactants, neutral water—soluble polysaccharides (e.g., dextran, Ficoll, celluloses), non—cationic poly(meth)acrylates, non—cationic polyacrylates, such as poly(meth)acrylic acid, and esters amide and hydroxyalkyl amides f, natural emulsifiers (e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, ux, cholesterol, xanthan, , gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g. bentonite [aluminum silicate] and Veegum [magnesium um 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 propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic tives (e.g. carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g. polyoxyethylene sorbitan monolaurate [Tween 20], polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan eate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan monostearate [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 te, and Solutol), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g. Cremophor), polyoxyethylene , (e.g. polyoxyethylene lauryl ether [Brij 30]), poly(vinyl—pyrrolidone), diethylene glycol monolaurate, anolamine oleate, sodium , potassium oleate, ethyl oleate, oleic acid, 2012/062222 ethyl laurate, sodium lauryl sulfate, ic F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, etc. and/or ations thereof. In certain ments, the emulsifying agent is cholesterol.

] Additionally, the ition may further comprise an apolipoprotein. Previous studies have reported 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 -based mechanisms. Mol Ther. 18(7): p. 1357—64. In n embodiments, the apolipoprotein is ApoA, ApoB, ApoC, ApoE, or ApoH, or an isoform thereof.

Liquid compositions e emulsions, microemulsions, solutions, suspensions, syrups, and elixirs. In addition to the APPL, the liquid composition may contain inert ts commonly used in the art such as, for example, water or other solvents, solubilizing agents and fiers 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, groundnut, corn, germ, olive, , and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures 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, injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable ation may also be a injectable solution, sion, or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a on 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 addition, 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 cellulose and 0.1% (v/v) Tween 80. The injectable composition can be sterilized, for example, by tion 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 , or a suppository wax which are solid at t temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the particles.

Solid compositions include capsules, tablets, pills, powders, and granules. In such solid compositions, the particles are mixed with at least one excipient and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as ol, d) disintegrating agents such as agar—agar, calcium carbonate, potato or tapioca , alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium nds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and es thereof. In the case of capsules, tablets, and pills, the dosage form may also comprise buffering . Solid compositions of a similar type may also be employed as fillers in soft and hard—filled gelatin capsules using such ents 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 gs 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 ingredient(s) only, or preferentially, in a certain part of the inal 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 gelatin 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 nts, pastes, creams, lotions, gels, powders, ons, sprays, inhalants, or patches. The APPL is admixed with an excipient and any needed preservatives or s 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 contain, in addition to the APPL, excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc, and zinc oxide, or mixtures thereof.

Powders and sprays can contain, in addition to the APPL, excipients such as lactose, talc, silicic acid, aluminum hydroxide, m silicates, and polyamide powder, or es of these substances. Sprays can additionally n customary propellants such as fluorohydrocarbons. ermal 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 rticles in a proper medium. Absorption enhancers 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 eutic, diagnostic, or prophylactic . Any chemical compound to be stered to a subject may be delivered using the complexes, picoparticles, nanoparticles, microparticles, es, 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, polynucleotide, targeting agent, isotopically labeled organic or inorganic molecule, e, logical agent, etc.

In certain embodiments, the agents are organic molecules with pharmaceutical activity, 6.57., a drug. In certain ments, the drug is an antibiotic, iral agent, anesthetic, steroidal agent, anti—inflammatory agent, anti—neoplastic agent, anti—cancer agent, antigen, vaccine, antibody, decongestant, antihypertensive, ve, birth control agent, progestational agent, anti—cholinergic, analgesic, anti—depressant, anti—psychotic, B—adrenergic blocking agent, diuretic, cardiovascular active agent, vasoactive 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.

Diagnostic agents include gases; metals; commercially available imaging agents used in positron emissions tomography (PET), computer assisted tomography (CAT), single photon emission computerized tomography, x—ray, fluoroscopy, and magnetic resonance imaging (MRI); and st agents. 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 — based materials.

Therapeutic and lactic agents include, but are not limited to, antibiotics, nutritional supplements, and es. Vaccines may comprise isolated proteins or peptides, inactivated organisms and viruses, dead organisms and s, genetically altered organisms or viruses, and cell extracts. Therapeutic and prophylactic agents may be combined with interleukins, eron, cytokines, and adjuvants such as cholera toxin, alum, Freund’s adjuvant, etc. Prophylactic agents e antigens of such bacterial organisms as Streptococccus pneumoniae, Haemophilus zae, Staphylococcus aureus, Streptococcus pyrogenes, Corynebacterium diphtheriae, Listeria togenes, 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 cholerae, Legionella pneumophila, Mycobacterium tuberculosis, Mycobacterium leprae, Treponema um, Leptospirosis interrogans, Borrelia rferi, Campliylobacterjejuni, and the like; antigens of such viruses as smallpox, influenza A and B, respiratory syncytial virus, parainfluenza, s, HIV, varicella—zoster, herpes x l and 2, galovirus, Epstein—Barr virus, rotavirus, rhinovirus, adenovirus, papillomavirus, poliovirus, mumps, rabies, rubella, coxsackieviruses, equine encephalitis, Japanese alitis, yellow fever, Rift Valley fever, hepatitis A, B, C, D, and E virus, and the like; antigens of fungal, protozoan, and parasitic organisms such as Cryptococcus neoformans, Histoplasma capsulatum, Candida albicans, a alis, Nocardia asteroides, Rickettsia sii, Rickettsia typhi, Mycoplasma pneumoniae, Chlamydial psittaci, Chlamydial 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, articles, picoparticles and nanoparticles, prepared therefrom, may be modified to e targeting 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 e. The targeting agent may be a protein, peptide, ydrate, glycoprotein, lipid, small molecule, nucleic acids, etc. The targeting agent may be used to target specific cells or s or may be used to promote endocytosis or phagocytosis of the particle. Examples of ing agents include, but are not limited to, antibodies, fragments of antibodies, low—density lipoproteins (LDLs), transferrin, asialycoproteins, gp120 envelope protein of the human immunodeficiency virus (HIV), carbohydrates, receptor s, sialic acid, rs, 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 nt, hydrophobic, hydrogen bonding, van der Waals, or other ctions) 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 polynucleotide (e. g., DNA, RNA, synthetic s of DNA and/or RNA, DNA/RNA hydrids, etc.). Polynucleotides or derivatives f 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 prevent the degradation of the polynucleotide. By lizing the charge on the backbone of the polynucleotide, the neutral or slightly—positively—charged complex is also able to more easily pass through the hydrophobic membranes (e.g., cytoplasmic, lysosomal, endosomal, r) of the cell. In certain embodiments, the complex is slightly positively charged. In certain embodiments, the x has a positive C—potential. 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 cleotide; 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 e, 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 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 polynucleotide. In n ments, the polynucleotide/APPL x 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 material by increasing nucleic acid g and negatively influence delivery by increasing toxicity. See, e.g., Incani et al., Soft Matter (2010) 6:2124—2138. In certain embodiments, the en:phosphate ratio (Le. the ratio between the amino groups present in the APPL, and the ate groups present 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 ments, the APPL:polynucleotide mass ratio is about 15:1. In certain embodiments, the APPL:polynucleotide molar ratio is between about 10:1 to about 400:1, inclusive. In certain embodiments, the olynucleotide 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, ive.

In certain ments, the complex may form a particle. In certain embodiments, the diameter of the particles ranges from 10—500 micrometers. In certain embodiments, the diameter of the les ranges from 10— 1200 micrometers. In certain embodiments, the diameter 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— 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 architecture 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, encapsulated by an APPL, or included in a composition comprising an APPL. The polynucleotide may be any c acid including, but not limited to, RNA and DNA. In certain embodiments, the cleotide is DNA. In n embodiments, the polynucleotide is RNA. In certain embodiments, upon delivery of the RNA into a cell, the RNA is able to ere with the expression of a specific gene in the biological cell.

In certain embodiments, the polynucleotide is an RNA that carries out RNA erence (RNAi). The phenomenon of RNAi is discussed in greater detail, for example, in the following references: ir 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, ; 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 interfering RNA). In certain embodiments, the polynucleotide is an shRNA (short hairpin RNA). In certain embodiments, the polynucleotide is an miRNA (micro RNA). Micro RNAs s) are genomically encoded non—coding RNAs of about 21 — 23 nucleotides in length that help regulate gene expression, particularly during pment. 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 cleotide is an antisense RNA.

In certain embodiments, the cleotide may be ed 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 hybridize, e. g., bind, under cellular conditions, with ar mRNA and/or genomic DNA, or mutants thereof, so as to inhibit expression of the encoded protein, e.g., by inhibiting transcription and/or translation. See, e. g., Crooke “Molecular mechanisms of action of antisense drugs” Biochim.

Biophys. Acta l489(l):31—44, 1999; Crooke “Evaluating the ism of action of antiproliferative antisense drugs” Antisense Nucleic Acid Drug Dev. 10(2): 123— 126, discussion 127, 2000; Methods in logy volumes 4, 1999. The binding may be by conventional base pair mentarity, 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 formation). 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 ed and/or ted using one or more of a large number of available algorithms. To give but a few examples, the following ces can be utilized to design and/or predict polynucleotides: algorithms found at Alnylum Online, Dharmacon 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 certain 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 ntially pure. In certain embodiments, 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., Ausubel et al., Current Protocols in Molecular Biology (John Wiley & Sons, Inc., New York, 1999); Molecular Cloning: A tory Manual, 2nd Ed., ed. by Sambrook, Fritsch, and is (Cold Spring Harbor tory Press: 1989). The polynucleotide may also be ed from natural s and purified from contaminating components found normally in nature. The polynucleotide may also be chemically synthesized in a laboratory. In certain embodiments, the polynucleotide is synthesized using rd solid phase chemistry.

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

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

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

These derivatives 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 analogs: oadenosine, 2—thiothymidine, inosine, pyrrolo—pyrimidine, 3— methyl adenosine, 5—methylcytidine, mouridine, CS—fluorouridine, ouridine, C5—propynyl—uridine, C5—propynyl—cytidine, C5—methylcytidine, 7—deazaadenosine, 7—deazaguanosine, 8—oxoadenosine, 8—oxoguanosine, O(6)—methylguanine, and 2—thiocytidine.

Modified 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 polynucleotides 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 prepared using synthetic chemistry in vitro.

The polynucleotides to be delivered may be in any form. For e, the polynucleotide may be a circular plasmid, a linearized d, a cosmid, a viral genome, a modified viral genome, an artificial some, etc.

] The polynucleotide may be of any sequence. In certain embodiments, the polynucleotide encodes a n or peptide. The encoded proteins may be enzymes, structural proteins, ors, soluble receptors, ion channels, pharmaceutically active proteins, cytokines, interleukins, antibodies, dy fragments, antigens, coagulation factors, albumin, growth factors, hormones, insulin, etc. The polynucleotide may also comprise regulatory regions to control the expression of a gene. These regulatory regions may include, but are not limited to, promoters, enhancer elements, repressor elements, TATA box, ribosomal binding sites, stop site for transcription, etc. In certain embodiments, the cleotide 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 ce 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 symptoms associated with such an infection. The cleotide of these vaccines may be combined with eukins, interferon, cytokines, and adjuvants such as cholera toxin, alum, Freund’s nt, etc. A large number of adjuvant compounds are known; a useful dium of many such compounds 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 ial organisms as Streptococccus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Streptococcus pyrogenes, bacterium 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 pneumophila, Mycobacterium ulosis, cterium leprae, ema pallidum, Leptospirosis interrogans, Borrelia burgdorferi, Campliylobacterjejuni, and the like; from such viruses as smallpox, za A and B, respiratory syncytial virus, parainfluenza, measles, HIV, varicella—zoster, herpes simplex 1 and 2, cytomegalovirus, Epstein—Barr virus, rotavirus, rhinovirus, irus, papillomavirus, poliovirus, mumps, rabies, rubella, coxsackieviruses, equine alitis, Japanese encephalitis, yellow fever, Rift Valley fever, hepatitis A, B, C, D, and E virus, and the like; and from such fungal, protozoan, and parasitic organisms such as coccus neoformans, Histoplasma capsulatum, Candida albicans, Candida tropicalis, Nocardia asteroides, tsia sii, Rickettsia typhi, Mycoplasma pneumoniae, Chlamydial psittaci, Chlamydial trachomatis, Plasmodiumfalciparum, Trypanosoma brucei, Entamoeba histolytica, Toxoplasma gondii, Trichomonas vaginalis, Schistosoma mansoni, and the like.

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

APPLs have several properties that make them particularly suitable for delivery, including: 1) the ability of an APPL to complex and ct” 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 encapsulate agents including, but not limited to, organic molecules (e.g., cholesterol, drugs), inorganic molecules, nucleic acids, proteins, peptides, polynucleotides, targeting agents, isotopically d organic or inorganic molecules, vaccines, immunological agents, 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), l 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 materials (e.g., polymers).

In certain embodiments, the diameter of the particles range from between 1 micrometer to 1,000 micrometers. 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 n embodiments, the diameter of the particles range from between from 10 micrometer to 100 micrometers. In certain embodiments, the er of the particles range from between from 100 micrometer to 1,000 micrometers. In certain embodiments, the les range from l—5 micrometers. In certain embodiments, the er of the particles range from between 1 nm to 1,000 nm. In certain embodiments, the diameter of the particles range from between from 1 nm to 100 nm. In certain embodiments, the diameter of the les 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 embodiments, the diameter of the particles range from n 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 n 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 certain embodiments, the diameter of the particles range from between from 10 pm to 100 pm. In certain embodiments, the diameter of the particles range from between from 100 pm to 1,000 pm. In certain 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 t evaporation, t tion, phase separation, simple and complex coacervation, and other s 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 ions used in preparing the particles may be altered to yield particles of a desired size or property (e.g., hydrophobicity, hydrophilicity, external morphology, “stickiness”, shape, etc). The method of preparing the particle and the conditions (e.g., solvent, temperature, concentration, 2012/062222 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 literature. See, e. g., Doubrow, M., Ed., “Microcapsules and Nanoparticles in ne and Pharmacy,” CRC Press, Boca Raton, 1992; Mathiowitz 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 particles 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 r contemplates use of APPLs in the preparation of micelles or liposomes. Any agent may be further included in a e or liposome. es 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 referred 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 es and liposomes.

In n embodiments, liposomes are formed through neous assembly.

In other embodiments, mes 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 self—close to form large, multilamellar vesicles (LMV). This ts interaction of water with the hydrocarbon core of the rs at the edges. Once these particles have formed, ng 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 Encylopedia ofNanoscience and Nanotechnology; Nalwa, H. S.

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

Rev. Biophys. Bioeng. 9:467—508, 1980; each of which is incorporated herein. The preparation of lipsomes involves preparing the APPL for ion, hydrating the APPL with agitation, and sizing the vesicles to achieve a homogenous distribution 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 r—derived film. This polymer—derived film is thoroughly 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 agitating 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 h a polycarbonate filter with a defined 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 ments, the application of the liposome is the delivery of polynucleotides.

The following scientific papers described other methods for preparing liposomes and es: Narang et al., “Cationic Lipids with Increased DNA Binding Affinity for Nonviral Gene er in Dividing and Nondividing Cells” Bioconjugate Chem. 16: 156—68, 2005; Hofland et al., “Formation of stable ic lipid/DNA complexes for gene transfer” Proc. Natl. Acad. Sci. USA 93:7305—7309, July 1996; Byk et al., “Synthesis, Activity, and Structure—Activity Relationship Studies of Novel Cationic Lipids for DNA Transfer” J. Med. Chem. 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 water—soluble polymers as delivery systems for poorly e drugs” Advanced Drug Delivery Reviews 56:1273—1289, 2004; Tranchant et al., “Physicochemical optimisation of plasmid delivery by ic lipids” J. Gene Med. 6:S24—S35, 2004; van Balen et al., ome/Water Lipophilicity: s, Information Content, and Pharmaceutical ations” Medicinal Research Rev. 24(3):299- 324, 2004.

Treatment Methods It is estimated that over 10,000 human diseases are caused by c 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; Leachman, 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 , severe hypercholesterolemia, and familial amyloidotic polyneuropathy. See, e.g., Frank— Kamenetsky, M., et al., Therapeutic RNAi targeting PCSK9 acutely lowers plasma cholesterol in rodents and LDL terol in nonhuman primates. Proc Natl Acad Sci U S A, 2008. ): p. 11915—20; Coelho, T., Familial amyloid polyneuropathy: new developments in genetics and treatment. Curr Opin Neurol, 1996. 9(5): p. 355—9. Since the discovery of gene expression silencing via RNA interference (RNAi) by Fire and Mello (Fire, A., et al., Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 1998. 391(6669): p. 806—1 1), there has been extensive effort toward developing therapeutic applications for RNAi in humans. See, e.g., Davis, M.E., The first targeted delivery ofsiRNA in humans via a self-assembling, extrin 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. 8; Tan, S.J., et al., ering Nanocarriers for siRNA Delivery. Small. 7(7): p. 841—56; 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 delivery 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 dicines.

Expert Opin Drug Deliv, 2008. 5(1): p. 25—44; and Thiel, K.W. and RH. Giangrande, Therapeutic applications ofDNA and RNA aptamers. 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 s for the treatment of various diseases. See, e.g., Burnett, J .C., J .J . Rossi, and K. Tiemann, Current progress 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 rs to therapy with nse and siRNA oligonucleotides.

Mol Pharm, 2009. 6(3): p. 686—95.

Thus, in another aspect, provided 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 es, disorders, or conditions, especially a system for delivering agents useful in the treatment of that particular e, disorder, or condition. se,” “disorder,” and “condition” are used interchangeably WO 63468 herein. In certain embodiments, the disease, disorder or condition from which a subject suffers is caused by an abnormality in a gene or some of the subject.

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

Exemplary disease, disorder, or conditions contemplated 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 ingredient in the composition.

Other agents, e.g., therapeutic agents, as described herein may also be classified as an active ingredient. In certain embodiments, the composition further ses, in addition to the APPL, a therapeutic agent useful in treating the e, er, or condition. In certain embodiments, the APPL encapsulates the other (therapeutic) agent. In certain embodiments, the APPL and the other peutic) agent form a particle (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 r includes an anti—cancer agent. Exemplary proliferative diseases include, but are not limited to, tumors, begnin sms, pre—malignant neoplasms (carcinoma in situ), and anat neoplasms (cancers).

] Exemplary cancers include, but are not limited to, acoustic neuroma, adenocarcinoma, adrenal gland cancer, anal cancer, angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma), appendix cancer, benign monoclonal gammopathy, biliary cancer (e.g., cholangiocarcinoma), bladder cancer, breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary , medullary carcinoma of the breast), brain cancer (e.g., meningioma; glioma, e.g., astrocytoma, endroglioma; medulloblastoma), bronchus cancer, carcinoid tumor, cervical cancer (e.g., al adenocarcinoma), choriocarcinoma, chordoma, craniopharyngioma, colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma), epithelial carcinoma, ependymoma, endotheliosarcoma (e.g., Kaposi’s sarcoma, multiple idiopathic hemorrhagic sarcoma), trial cancer (e.g., uterine cancer, uterine sarcoma), esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett’s adenocarinoma), Ewing’s sarcoma, eye cancer (e.g., intraocular melanoma, retinoblastoma), familiar hypereosinophilia, gall bladder , gastric cancer (e.g., h adenocarcinoma), gastrointestinal stromal tumor (GIST), head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma (OSCC), throat cancer (e.g., eal cancer, pharyngeal cancer, aryngeal cancer, oropharyngeal cancer)), hematopoietic s (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 c 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 non—Hodgkin lymphoma (NHL) (e.g., B—cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B—cell lymphoma (DLBCL)), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic ma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B—cell lymphomas (e.g., mucosa—associated id tissue (MALT) lymphomas, nodal marginal zone B—cell lymphoma, splenic marginal zone B—cell lymphoma), 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 lymphoma and primary l nervous system (CNS) lymphoma; and T—cell NHL such as precursor T— blastic lymphoma/leukemia, peripheral T—cell lymphoma (PTCL) (e.g., cutaneous T— cell lymphoma (CTCL) (e.g., mycosis fungiodes, Sezary syndrome), angioimmunoblastic T— cell lymphoma, odal natural killer T—cell lymphoma, pathy type T—cell lymphoma, subcutaneous panniculitis—like T—cell lymphoma, anaplastic large cell lymphoma); a mixture 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, atory roblastic tumors, immunocytic 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), elioma, myeloproliferative disorder (MPD) (e.g., polycythemia Vera (PV), essential thrombocytosis (ET), agnogenic d metaplasia (AMM) a. k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)), neuroblastoma, neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis), neuroendocrine cancer (e.g., gastroenteropancreatic neuroendoctrine tumor ET), 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 , Islet cell tumors), penile cancer (e.g., Paget’s e of the penis and scrotum), pinealoma, primitive neuroectodermal tumor (PNT), prostate cancer (e.g., prostate adenocarcinoma), rectal cancer, myosarcoma, salivary gland cancer, skin cancer (e.g., squamous cell carcinoma (SCC), acanthoma (KA), melanoma, basal cell carcinoma (BCC)), small bowel cancer (e.g., appendix cancer), soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, 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 d, papillary thyroid carcinoma (PTC), medullary thyroid cancer), urethral cancer, vaginal cancer and vulvar cancer (e.g., Paget’s disease of the vulva).

] Anti—cancer agents encompass biotherapeutic anti—cancer agents as well as chemotherapeutic agents.

Exemplary biotherapeutic anti—cancer agents include, but are not limited to, interferons, cytokines (e.g., tumor necrosis factor, interferon 0t, interferon y), vaccines, hematopoietic growth factors, monoclonal serotherapy, 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 uzumab), T—DMl, AVASTIN (bevacizumab), ERBITUX (cetuximab), VECTIBIX (panitumumab), RITUXAN (rituximab), BEXXAR (tositumomab)).

Exemplary chemotherapeutic agents include, but are not limited to, anti— estrogens (e.g. tamoxifen, raloxifene, and megestrol), LHRH agonists (e.g. goscrclin and leuprolide), anti—androgens (e.g. de and bicalutamide), ynamic therapies (e.g. vertoporfin (BPD—MA), phthalocyanine, ensitizer Pc4, and oxy—hypocrellin A (2BA—2—DMHA)), nitrogen ds (e.g. cyclophosphamide, ifosfamide, trofosfamide, mbucil, estramustine, and melphalan), nitrosoureas (e.g. tine (BCNU) and lomustine (CCNU)), alkylsulphonates (e.g. busulfan and treosulfan), triazenes (e.g. dacarbazine, temozolomide), platinum containing nds (e.g. cisplatin, carboplatin, oxaliplatin), vinca alkaloids (e.g. vincristine, stine, vindesine, and vinorelbine), taxoids (e.g. axel or a paclitaxel equivalent such as nanoparticle albumin—bound paclitaxel (ABRAXANE), docosahexaenoic acid bound—paclitaxel (DHA—paclitaxel, exin), polyglutamate bound—paclitaxel (PG—paclitaxel, paclitaxel poliglumex, CT— 2103, ), 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 glucose—conjugated paclitaxel, e.g., 2'—paclitaxel methyl 2—glucopyranosyl succinate; docetaxel, taxol), ophyllins (e.g. etoposide, ide phosphate, teniposide, topotecan, 9—aminocamptothecin, camptoirinotecan, irinotecan, crisnatol, mytomycin C), anti—metabolites, DHFR inhibitors (e.g. methotrexate, dichloromethotrexate, trimetrexate, xate), IMP ogenase inhibitors (e.g. mycophenolic acid, tiazofurin, ribaVirin, and EICAR), ribonuclotide reductase inhibitors (e.g. hydroxyurea and deferoxamine), uracil analogs (e.g. ouracil (S—FU), floxuridine, doxifluridine, ratitrexed, tegafur—uracil, capecitabine), ne 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, peplomycin), anthracycline (e.g. daunorubicin, doxorubicin, pegylated liposomal bicin, idarubicin, icin, pirarubicin, zorubicin, ntrone), MDR inhibitors (e.g. verapamil), Ca2+ ATPase inhibitors (e.g. thapsigargin), imatinib, thalidomide, lenalidomide, ne kinase tors (e.g., aXitinib (AG013736), bosutinib (SKI—606), cediranib (RECENTINTM, AZD2171), dasatinib (SPRYCEL®, BMS—354825), erlotinib (TARCEVA®), gefitinib (IRESSA®), imatinib (Gleevec®, CGP57148B, STI—571), lapatinib (TYKERB®, TYVERB®), lestaurtinib (CEP—701), neratinib 72), nilotinib (TASIGNA®), semaxanib (semaXinib, SU5416), sunitinib (SUTENT®, SU11248), toceranib (PALLADIA®), vandetanib (ZACT]MA®, ZD6474), vatalanib (PTK787, ), zumab (HERCEPTIN®), zumab (AVASTIN®), rituXimab (RITUXAN®), cetuXimab (ERBITUX®), panitumumab (VECTIBIX®), ranibizumab (Lucentis®), nib (TASIGNA®), sorafenib (NEXAVAR®), everolimus (AFINITOR®), alemtuzumab (CAMPATH®), gemtuzumab ozogamicin (MYLOTARG®), temsirolimus (TORISEL®), ENMD-2076, PCI—32765, AC220, dovitinib lactate (TKI258, CHIR-258), BIBW 2992 (TOVOKTM), SGX523, PF—04217903, PF-02341066, PF-299804, EMS-777607, ABT-869, MP470, BIBF 1120 TEF®), AP24534, JNJ-26483327, MGCD265, DCC—2036, EMS-690154, CEP-11981, 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), rolimus, AP23573 (Ariad), AZD8055 (AstraZeneca), BEZ235 (Novartis), BGT226 (Norvartis), XL765 (Sanofi 2012/062222 Aventis), PF—4691502 (Pfizer), 0 (Genetech), SF1126 (Semafoe) and 081—027 (081)), oblimersen, gemcitabine, carminomycin, leucovorin, pemetrexed, cyclophosphamide, dacarbazine, procarbizine, prednisolone, dexamethasone, campathecin, plicamycin, asparaginase, aminopterin, methopterin, porfiromycin, melphalan, leurosidine, leurosine, mbucil, trabectedin, procarbazine, discodermolide, carminomycin,, aminopterin, and hexamethyl ne.

In certain embodiments, the condition is an inflammatory disorder and, in certain ments, the composition further includes an anti—inflammatory agent. The term “inflammatory disorder” refers to those diseases, disorders or conditions that are terized 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, diffuse, disseminated, exudative, fibrinous, fibrosing, focal, granulomatous, hyperplastic, hypertrophic, interstitial, atic, necrotic, obliterative, parenchymatous, plastic, productive, proliferous, pseudomembranous, purulent, sclerosing, seroplastic, serous, simple, specific, subacute, suppurative, toxic, traumatic, and/or ulcerative inflammation. ary inflammatory disorders include, but are not limited to, inflammation associated with acne, anemia (e.g., aplastic anemia, haemolytic autoimmune anaemia), asthma, arteritis (e.g., polyarteritis, temporal arteritis, periarteritis nodosa, Takayasu’s arteritis), arthritis (e.g., crystalline arthritis, osteoarthritis, tic arthritis, gouty arthritis, reactive tis, rheumatoid arthritis and Reiter’s arthritis), ankylosing spondylitis, amylosis, amyotrophic lateral sclerosis, autoimmune diseases, allergies or allergic reactions, sclerosis, bronchitis, is, c prostatitis, ctivitis, Chagas disease, c obstructive pulmonary disease, cermatomyositis, diverticulitis, es (e.g., type I diabetes mellitus, type 2 es 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, n headaches), ileus (e.g., postoperative ileus and ileus during sepsis), idiopathic thrombocytopenic purpura, interstitial cystitis (painful bladder me), gastrointestinal disorder (e.g. , selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic gastrointestinal disorders (e.g., eosinophilic esophagitis, eosinophilic gastritis, philic gastroenteritis, eosinophilic colitis), tis, diarrhea, gastroesophageal reflux disease (GORD, or its m GERD), atory bowel e (IBD) (e.g., Crohn’s disease, ulcerative colitis, collagenous colitis, lymphocytic s, ischaemic colitis, diversion colitis, Behcet’s syndrome, indeterminate colitis) and inflammatory bowel me , lupus, multiple sclerosis, morphea, myeasthenia gravis, myocardial ia, nephrotic syndrome, pemphigus vulgaris, pernicious aneaemia, peptic ulcers, polymyositis, primary biliary cirrhosis, neuroinflammation associated with brain disorders (e.g., Parkinson’s disease, Huntington’s disease, and Alzheimer’s disease), prostatitis, chronic inflammation associated with cranial radiation injury, pelvic inflammatory disease, reperfusion injury, regional enteritis, tic fever, systemic lupus erythematosus, schleroderma, scierodoma, sarcoidosis, spondyloarthopathies, Sjogren’s syndrome, thyroiditis, lantation rejection, tendonitis, trauma or injury (e.g., frostbite, chemical nts, toxins, scarring, burns, physical injury), vasculitis, vitiligo and Wegener’s omatosis.

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

In certain embodiments, the condition is an autoimmune disorder and, in certain embodiments, the composition further includes an immunomodulatory agent. Exemplary autoimmune disorders include, but are not limited to, arthritis (including rheumatoid arthritis, spondyloarthopathies, gouty arthritis, degenerative joint diseases such as osteoarthritis, systemic lupus erythematosus, Sjogren's me, ankylosing litis, undifferentiated spondylitis, Behcet's disease, haemolytic autoimmune anaemias, multiple sclerosis, amyotrophic lateral sclerosis, amylosis, acute painful shoulder, tic, and juvenile arthritis), asthma, atherosclerosis, osteoporosis, bronchitis, tendonitis, bursitis, skin condition (e.g., psoriasis, eczema, burns, dermatitis, pruritus (itch)), enuresis, eosinophilic e, gastrointestinal disorder (e.g. , selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic intestinal disorders (e.g., eosinophilic esophagitis, eosinophilic gastritis, eosinophilic gastroenteritis, eosinophilic colitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, or its synonym GERD), inflammatory bowel disease (IBD) (e.g., Crohn's disease, ulcerative colitis, collagenous s, lymphocytic colitis, ischaemic s, diversion colitis, '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; gastroesophageal reflux disease (GORD, or its synonym GERD); eosinophilic esophagitis, gastroparesis such as diabetic gastroparesis; food intolerances and food allergies and other functional bowel disorders, such as non—ulcerative dyspepsia (NUD) and non—cardiac chest pain (NCCP, including costo— chondritis)).

In certain ments, the condition is a painful condition and, in certain embodiments, the composition further includes an analgesic agent. A “painful condition” includes, but is not limited to, athic 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 post—operative pain, e.g., pain arising after hip, knee, or other replacement surgery), pre —operative pain, stimulus of nociceptive receptors (nociceptive pain), acute pain (e.g. , m and ent acute pain), noninflammatory pain, inflammatory pain, pain associated with cancer, wound pain, burn pain, postoperative pain, pain associated with medical ures, pain resulting from pruritus, painful bladder syndrome, pain associated with premenstrual dysphoric disorder and/or premenstrual syndrome, pain associated with chronic fatigue syndrome, pain associated with pre—terrn labor, pain associated with withdrawl symptoms from drug addiction, joint pain, tic pain (e.g., pain associated with crystalline arthritis, osteoarthritis, psoriatic arthritis, 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, inflammatory pain, athic pain, etc.). In some embodiments, a particular pain can te. In other ments, the painful condition comprises two or more types of pains without one dominating. A skilled clinician can determine the dosage to e a therapeutically effective amount for a particular subject based on the painful condition.

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

] In n embodiments, the condition is a liver disease and, in certain 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., acetaminophen—induced liver injury), hepatitis (e.g. , chronic hepatitis, viral hepatitis, alcohol—induced hepatitis, mune hepatitis, steatohepatitis), non—alcoholic fatty liver disease, alcohol—induced liver disease (e.g., alcoholic fatty liver, lic hepatitis, alcohol— related cirrhosis), hypercholesterolemia (e.g., severe hypercholesterolemia), transthyretin— related hereditary amyloidosis, liver cirrhosis, liver cancer, primary biliary 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 embodiments, the composition r es an agent useful in a al 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, , child, adolescent) or adult t (e.g., young adult, middle—aged adult or senior adult)) and/or other non—human animals, for example s [e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); and commercially nt mammals such as mice, rats, hampsters, cattle, pigs, horses, sheep, goats, cats, and/or dogs] and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys). In certain ments, the subject 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” contemplate 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 progression of the disease, disorder or ion (“therapeutic treatment”), and also contemplates an action that occurs before a subject begins to suffer from the specified disease, disorder or condition (“prophylactic treatment”).

In general, the “effective amount” of an active ingredient refers to an amount ient to elicit the desired biological response. As will be iated by those of ry skill in this art, the effective amount of a compound of the ion may vary depending 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 asses therapeutic and prophylactic ent.

As used herein, and unless otherwise 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 ion. A therapeutically effective amount of an active ingredient means an amount of the active ingredient, alone or in combination with other agents or therapies, which provides a therapeutic benefit in the treatment of the disease, disorder or condition. The term peutically effective ” 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, er or condition, or one or more symptoms associated with the disease, disorder or condition, or prevent its recurrence. A prophylactically effective amount of an active ingredient means an amount of the active ient, alone or in combination with other agents or ies, which provides a prophylactic benefit in the prevention of the disease, disorder or condition. The term ylactically effective amount” can encompass an amount that improves l prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.

The active ingredient may be administered in such amounts, time, and route deemed necessary in order to achieve the desired result. The exact amount of the active ingredient will vary from t to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular active ingredient, its mode of stration, its mode of activity, and the like. The active ingredient, whether the APPL itself, or the APPL in ation 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 attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject will depend upon a variety of s including the disorder being treated and the ty 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 ion of the ic active ingredient employed; the on 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 , including oral, intravenous, intramuscular, intra—arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, ermal, , intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, enteral, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or l. In general the most riate route of administration will depend upon a variety of factors including the nature of the active ingredient (e.g., its stability in the environment of the gastrointestinal tract), the condition of the t (e.g., whether the subject is able to tolerate oral administration), etc.

The exact amount of an active ingredient required to achieve a therapeutically or prophylactically ive amount will vary from subject to subject, ing on species, age, and general condition of a subject, severity of the side effects or disorder, ty of the particular compound(s), mode of administration, and the like. The amount to be administered to, for example, a child or an cent can be ined by a medical practitioner or person skilled in the art and can be lower or the same as that stered 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 understood that these examples are for illustrative purposes only and are not to be construed as limiting this invention in any manner.

Amino acid-, peptide-, and polypeptide-lipids (APPL) for drug delivery To address the challenges associated with delivery efficiency, specificity, and toxicity of biological agents, we ped 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 approach to develop new cationic lipids (lipidoids) for siRNA delivery. See, e. g., Akinc, A., et al., A combinatorial library of lipid-like materials for delivery ofRNAi eutics. Nat Biotechnol, 2008. 26(5): p. 561—9; 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; Siegwart, D.J., et al., Combinatorial synthesis of chemically diverse core-shell nanoparticles for intracellular ry. Proc Natl Acad Sci U S A. 108(32): p. 12996—3001. A number of these compounds have shown significant ing 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 ic 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 isms. 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 compounds possess 12 or more s 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 efficacy, tissue and cell—type selectivity, and tolerability, new chemical lds need to be ed and investigated.

Amino acids are natural building blocks of peptides and ns in nature.

Amino acid tives can be metabolized by the human body; therefore, these materials are likely well tolerated and safe as therapeutics. Additionally, peptides play significant roles in membrane transport, endogenous cellular signaling and trafficking pathways, and offer tremendous potential in leveraging such interactions to enhance the delivery efficiency of systems which orate peptide moieties. e 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 therapeutic medicines in the clinic for diverse diseases. Studies have shown that it is feasible to apply amino acid—derivatives for gene delivery or siRNA delivery. See, e. g., Prata, C.A., et al., Lipopliilic peptides for gene delivery. Bioconjug Chem, 2008. 19(2): p. ; Adami, R.C., et al., An amino ased amplioteric mal 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 delivery. Mol Ther. 20(3): p. . Combining the advantages of both natural properties of amino acids and structural features of lipidoids, we applied 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 trate 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. Preparation of Compounds of Formula (I)-(III). Conjugation to formula (i).

A mixture of amino acids, es or polypeptides and the conjugating reagent (an epoxide, ne, 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 mixture was purified by flash column chromatography. If amino acids, peptides or ptides 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 Y 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 II). Conjugation to formula (ii).

A mixture of amino acids, peptides 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 d for 2 hours to 2 days. The reaction solution was concentrated with silica gel and purified 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 2012/062222 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 RL’X\n/\/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 conjugating reagent (aldehyde) (a ratio of 1.5:1 to 3:1 des 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 purified with flash column tography.

Scheme K.

O O O R1 R1 0 Ac)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 Ac)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 condensation of a 1,2— diamine with an activated oxalic acid, wherein X1 is a leaving group, e.g., bromo, , or iodo, to provide the cyclized product. Groups of formula (i), (ii), or (iii), may be installed WO 63468 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 scaffold, 6.57., R2 groups, may be led prior to ation. For example, 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 nds of Formula (V) Compounds of a (V), and (VI) may be prepared 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 scaffold, 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 Q.

R2 Q ‘NH x1 R1—< + R1—<N [NH X1 l R2 Q 2HX1 1,1-diamine malonyl derivative Method 6. Preparation of Compounds of Formula (V1) Compounds of Formula (VI) may be ed via condensation of a hydrazine with an activated succinic acid, wherein X1 is a leaving group, e.g., bromo, chloro, or iodo, to e 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 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 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 ne 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 3)(CH2CH3) ORA4 INZof; O50)>A Leucine 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, Tyrosine Y 2 ’a Tryptophan W / / N HN * R6 and R7 are hydrogen in the precursor, and, upon conjugation, are independently selected from the group ting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, ally 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 ting group when ed 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 ne K—(K)n—K As above; n = 3—12 (500—2000 g/mol) PK—SOO polysine K—(K)n—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 ne 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 polyarginine R-(R)n-R (5000—15000) PR-5000 linear ine—histidine linear H—H cyclic histidine—histidine cyclic H—H Table 2. Peptides and Polypeptides Name, Symbol Amino acid polyhistidine H-(H)n-H H2N ORA4 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 glutamlc ac1d—lys1ne. . . . llnear EK. HzN/fif H N/En/N2 OH linear phenylalanine— linear PK 0 lysine N H2 /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 Table 2. Peptides and Polypeptides Name, Symbol Amino acid ZIf3“ IN20:2—\' 0I linear nine—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 tyrosine—lysine linear YK H2N OH linear lysine—threonine linear KT 0 H2N OH linear lysine—valine linear KV 0 H2N OH Table 3. ating reagents Table 3. Con'unatin rea_ents Name ure 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 ts Name Structure Synthetic Procedures Example 1. Synthesis of APPLs Schemes A—R show the general synthetic routes to APPLs of Formula (I) to (VI), of the present invention. Application of these methods generated a variety of APPLs, depicted in Tables 4 and 5.

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

For example, K—E12 represents the reaction of lysine with 1,2—epoxydodecane.

WO 63468 a \\\\\\.\ AXE“ 2012/062222 IIIIIIIIIIIIIIIIII L»5L»Hfifififififififififififififififififififififimv\\\\\\\\\\\\\\\\\xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\L\\\\\\v\\\f\\yd»5L»L»5L»5L»LavLavLav5L»L»L»L»5L»5L»LavLavLav5L»L»5L»5L»5L»LavLav5L»5L»L»5L»5L»5L»LavLavLuvHfififififififififififififififififififififimv\\\\\\\\\\\\\\\\\\\\\\Vfi.. \x:Nanmwm., .4 . .m\: \\\\\\\\\\\\\\\\\\\\\\\\4\\,\\\\\ MMMRNMxmxx .

I81*\f “Wm., ., . xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx¥xxx\nxxxxxxxxxxxxxxxx\\\\¥\\\\\\\\\\\\\\\,\\\\ ‘ Mn»m.\\\.mx . ux«xu« ‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘ .MNMM:. \w.K Aw~\ gm u««xux 3th . >0VF.

WO 63468 kéww mm E‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘\k\‘:‘kkkkkkkkk‘:a. gmmfiww fix“ fix 2012/062222 .mV...

Lx.» «(r$3.“ SEHMS my\w fi\\\\\\\\\\\\\\\\\aaaaaaaaaaaaaaaaaaaaaaaa"\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\“.uuuuuuuuuuuuuuuuuuuuuuwwuuuuuuuuuuuuuuuuuuuuuuu xxx»xxxxxxxxxxxxxxxxxxxxxxxx smvmfw .K\‘\“\‘\“\‘\“\‘\“\‘\“\‘. x»xxxx»xxxx»xxxx»xxxx»xxxx»xxxxxxxxx»xxxxxxxxxxxxxxxxxxxxxxxxxxx “$mewa.........mcmmfiwfi ‘\“\‘\“\‘\“\‘\“\‘\“\‘\“\;\“\‘\“\‘\“\‘\“\‘\“\‘\“\‘\‘. xxxxx»xxxx»xxxx»xxxx»xxxxxxxxxxxxxxxxxxxxxxxxxx mxxmwmmum“ “v \‘\“\‘\“\‘\“\‘\“\‘\“ WO 63468 nnnnnnnn.‘ \ ,k»--------~.... .wc». .v..3..v..3..v..3..v..3..v..3..v..3..v..3..v..3..v..3..v..3..v.-----------~u... ‘u«u? ........xi\xxExxx{xixiiiixifiiii “wwm‘wa‘ a Em“ M xix... fi$§u ........xixxxExxx{xixiiiiiiiii wwm“§§m§ xv. {2... mg ......................................................................................vvvvvvvvvvvvvvvvvvvvvvExxxxxxxxxxxxxxxxxxxx»x»Exttxttxttxt‘........................................

M ..............................t................................ mxxmwww “MS xxx i“ ...............................................

‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘ .......................................................................................................................... \A\\\\v‘~~~~ 4% «unnnnnnnnnnnuu\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"»‘»"»‘»"»‘»"»‘»‘mwwwwwwwwwwwwwwwwwwwwuuuuuuuuuuuuuuuuuuuuuv\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ aw ¢xa ANN”, N.» Mm “,‘““““““““‘““““““““““‘““““““““““‘““““““““““‘““““““““““"+“““““““““‘““““““““““‘““““““““ x»o x»o +"""‘“"“"""‘“"“"""““““““““““““\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\«\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\‘\\\\\\\\\\\\\\\\\\\\\\\\\\1 2012/062222 ‘‘‘‘‘‘‘‘k‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘ “$3“ kKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkK:3::::§:===awwwwfim vnnnnnnnnnnnnnnnn.\\\\\\\\\\\\\\\\\\\\\\\\x\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\\x\\\uuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuu\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ .33». \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ kimffim \\\\x\\\\\\\\\\\\\\\\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\‘c\\\\\\\\\\\\\\\\\\\filmy“ x\x\\\\x\\\\x\\\\x\\\\x\\\¢\\\\\\\\\\\\\\\\\\\\ w¢x fim NH \\\\\\\\\~\\\\\\\\\"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“‘““““““““““““ 2012/062222 v»fififlpfim.x ecu. \\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ .fiwfiafifim z“ 3 WO 63468 ‘\ a 3‘ng \\\\\\§\ $221K. kw“ 3‘ e22. ii??? WO 63468 KkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKkKk:5§:=::==== ..1................................................................................................................................................................ \\\\\\\\\\\\\\\mmmmmmmmmmmmmmmmmmmm.xxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixxxixMmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm.xxxix{iiiiiiiiiii 8:3 mm.“ waxwwfifi (“-i 2012/062222 ”warn”; \ ¢ \ M} \ ‘Q ........................4.......................... M ............................... “u“‘u "u"‘u.x‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u"‘u‘“u““u“u““u“u WO 63468 §- 00'» £3 ‘ at; S ‘ Si N \\.\.\.\.\' * ..- m ‘ . . A» gm“ 1w»! E‘ifimfimi E WO 63468 6%.» NM, mum w w www.mymfi \\\\\\\\\\\\\\\\\\\\\\\\\\\v\\\u\\\\\\\\\\\\\\\\\\\\\\\\\\ Lam.»«Ram\\\\\\\\memwmwwm m3 \\\\\\\\\\\\\\\\\\\ «Nam. .M .................................................................................................................................................v4v4vv4v4vv4v4vv4v4vv4v4vv4vvvvvvvvvvvvvvvvvvvvvvvv...................................................v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4v4vv4vvvvvv;uuuuuuuuuuuuuuuuu 44444444444444444444444444444444444444444444444444WWW44444444444444444444444444444444444444444444444444444444444444444444444«44;;.v.v.v.v.v.v.v.v.v.v.v.v.v.v.v.v.v( fiién \\\\\\\\\ ""“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘““““““““““““ $1??? 2/5321: 2 \\\\\\\\\\\\\|||||||||||||||||||||||||||||||||||||..............................................................................................||||||||||||||||||||||||||||||||||||||||||||||||||||||||n.......................................................................................................................................L.....L. sxsxssxsxssxsxs ‘\\\\\\\\V {\K.12 imccqx ”rim WO 63468 »"K.

S:x: {.. < “““N‘ \xwfigr .w,.m\ \\\\ \- . '\ wwmfim wgfiwam x» Nu m """"‘."."““.“.“““.“.““““‘.“““"‘.""""‘."."““.“.“““.“.“““"‘.""‘.................."““.“.“““.“.““““‘.““““‘.““““‘.“ «««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««.uuuuuuuuuuuuuuuuuu«««««««««««««««««««««««««««««««««««««««««««««««««««« . ..............................\............................... “““.“.““““‘.“““"‘.*"""".“.“““.“.“““.“ Rmfi . ,me “figmmwmfiw tf'wi r3 m ‘««««««««««««««««««««««««««««««\««««««««««««««««««««««««««««««« ......................... ““.“.“““.“.“““‘ w «««««««««««««««««««««««««« ................... ‘.“.“““.“.““ Km «««««««««««««««««««« WO 63468 \\\\\\\\\ “nun“- T“ .x ‘3‘ \u Eggst‘!"""!‘!"""!‘!"""!‘!"""!‘!"""""~»--~»»»»~»--~»»»»~»--~»»»»~»~tttttttttttt"!‘!"""!‘!"""!‘!"""!‘!"""!‘!"""‘»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--~»»»»~»--tttttttttttt ttmfittt ..‘«kw!» fl.\. mam» \‘xxxxxxxx‘xxx‘xxl::.::.::.::.::.:.a.\.\.\.\.\RRRRRRRRRRRD...........................................................nwwwwn«QQQQQQQwQQQDi.hi.hi.hi.hi.hih................................. .............................. \mwfimmmwmwxmam ..............................+......................... x ................... .xxx ‘‘‘‘‘‘‘‘‘ 2012/062222 wwwwwwwwwwwwv.....................................................................................................h......p..p............................................................................................................. \~~~~~~\ ¢.~.~.~.\~.~.‘ \‘ kahuna}?i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i“‘{ii‘i‘i‘i‘i‘} .............................. ‘3. ‘6 \ \‘o ................................ can“ mm {V\ (Mmm "i"‘i"‘i"‘i"‘i"‘i‘«‘i"‘i“‘{ii‘i‘i‘i‘i‘} ......................p...mkwwmw M. ‘i{{{{{““““{“‘ ............h......* mm. {““““““““‘J 2012/062222 «~\\ \‘sss \ -:w .\\\~.\\ la...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a...a............................ 23,.yams'I. 34 E::3::3::3::3::3::3::3::3::3::3::3:"""‘33:33:33::::3::3::3:""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""‘33:33:33? ‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘‘ Wmfi as . ......... ..

T__\_\__\_\__\_»\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.........‘......... \\\\\\\\\Ammmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm. g .w é ‘¢\\\\\\\\ Q........¢ h§§§mm $.me ‘\\\\\\\\\\' gamma ....h.... ................................................................................................................................ anuuuuuuuuuuuuuuuuuuuuuuK vveueeee: ‘\\\\\\\\\‘ .\.\.\.\.\’ \\\\\\\\\ “"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘““““““““““““‘«x‘uuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuw............................................................‘;‘;;‘;‘;;‘;‘;;‘;‘;;‘;‘;;‘;‘;‘uuuuuuuuuuuuuuuuuuuuuuuuuuuuuw.................................u...............................

........................................................... WO 63468 \x\«{3 \_ \....\“ \...........X r. \x wwwwwww mfififi xx{xxxmxxxxxxxxxxxxxxxxxxm "‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘i"‘+"‘i‘“i““ii‘i‘i‘i‘i mwx n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n"‘n“““nnnn‘nnnn .fiwwfififiwmmm WO 63468 -. n.- ' 06}\: .~.~.~.~.~.\_ _.\sssssss}._ ¢ \ ‘ \_ \MM ...........................................................................................................................................................1,if,»if,»if,»if.»if.»if.»if.»if.»nannnnnnnnn,,,,,,,,,,,,,,,, ‘4“: .h....h. ""“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘““““““““““““ :33. ‘...................A 2012/062222 .........................................................................................................................................................................................................................................................................................................................................-.r.r”””””” S“\“\“\ .V". .6 F‘\\\\\\\\\\‘I\\A\\\\\\‘ 553‘. ....h.... “"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘“"‘““““““““““““‘ Table 5.

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+ 97 484.4327 2 E—E12 C29H56NO5+ 53 498.4117 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 N205+ 667 .5984 667.5894 3 P—E12 C17H32NO2+ 282.2428 282.2585 1 Q—E12 C29H57N204+ 497.4313 497.4268 2 R—E12 9N405+ 893.8392 893.8400 4 cKG—E12 C32H64N304+ 554.4891 554.4852 2 cKT—E12 C34H68N305+ 598.5153 598.5179 2 2 C39H70N305+ 660.5310 660.5350 2 cLK—E12 C36H72N304+ 610.5517 610.5556 2 cDK—E12* N306+ 640.5259 640.5316 2 2 N304S+ 628.5082 628.5072 2 cKV—E12 C35H70N304+ 596.5361 596.5330 2 cAK—E12 C33H66N304+ 568.5048 568.4992 2 cEK—E12 C35H68N306+ 626.5103 626.5053 2 cIK—E12 C36H72N304+ 610.5517 610.5501 2 cSK—E12 C33H66N305+ 584.4997 584.5029 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 6 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+ 458.4026 458.3857 2 D—A12 C28H56NO4+ 470.4204 470.4188 2 E—A12 C29H58NO4+ 484.4360 484.4319 2 I—A12 C30H62NO2+ 468.4775 468.4714 2 K—A12 C54H111N202+ 819.8640 819.8657 4 L—A12 NO2+ 468.4775 468.4752 2 M—A12 C29H60NO2S+ 486.4339 486.4318 2 N—A12 C28H57N203+ 64 469.4328 2 P—A12 C17H34NO2+ 284.2584 284.2512 1 Q—A12 C29H59N203+ 483.4520 483.4543 2 R—A12 C42H87N402+ 679.6824 679.6783 3 KK—A12 C84H171N403+ 1284.3346 1284.3458 6 2 C114H231N604+ 1748.8051 1748.8340 8 2 C60H121N402+ 929.9484 929.9445 4 A—O12 C18H36NO4+ 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 C24H40NO4+ 406.2952 406.2896 1 H—012 C36H66N306+ 46 636.4969 2 K—O12 C66H127N2010+ 1107.9485 1107.9417 4 M—O12 C20H40NO4S+ 390.2673 390.2628 1 N—012 C19H37N205+ 373.2697 373.2668 1 P—012 C20H38NO4+ 356.2795 356.2779 1 Q—012 C20H39N205+ 387 .2853 387.2831 1 R—O12 N404+ 415.3279 415.3235 1 S—012 NO5+ 346.2588 346.2521 1 T—012 C19H38NO5+ 44 360.2733 1 Chemical formula Observed V—012 C20H40NO4+ 358.2952 358.2905 W—Ol2 N204+ 445.3061 445.3010 * formation of ethyl ester. Compounds derived from poly—L—lysine are not included. ary compounds of Table 5: OH OH C10"‘21/g C10H21’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 WO 63468 C10"121/g C10H21 C10H21/</N CH C1on1 L-E12 M-E12 P-E12 R-E12 C10H21’g O OH OH /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 cKV-E12 2 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 2 OH OH O HOWNH Nj/j/C10H21j/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 WO 63468 ( OH rN OH NH C11H23 W-A12 OH Y_A12 C11H23 W O (312st N ('312st (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 2012/062222 O O C312H25/ O N C12H25/ OH K-O12 O N C12H25/ 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 compound 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 solvents were evaporated under reduced re and the TFA salts in DMF (3.5 mL) were added dropwise to ne (100 mL) at 0 0C. The reaction mixture was slowly warmed to room temperature and stirred for overnight. The solvents were evaporated under reduced pressure 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, ), 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).

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 degassed for 5 mins and hydrogen gas introduced. The reaction mixture stirred at rt overnight and was then filtered through a layer of Celite, 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), .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 ated in the ave oven at 150 0C for 5 h. The mixture was purified by flash column tography 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). e 3. Synthesis of Compound D It is envisioned compound D can be sized by reaction of 23 with Lawesson’ s reagent in dry toluene. 23 D Example 4. Synthesis of Compound E It is oned compound E can be synthesized by reaction of 23 with hydroxylamine hydrochloride or other substituted amines in methanol. 23 E Biolo ical s 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 concentration 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 ed against PBS to remove ethanol and exchange buffer.

Formulation B APPLs were formulated with cholesterol (Sigma—Aldrich), DSPC (1,2— distearoyl—sn—glycero—3—phosphocholine, Avanti), mPEG2000—DMG (synthesized 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 lled Microflnidic Formnlation. J Am Chem Soc. Formulations were then dialyzed against PBS in 3,500 MWCO dialysis cassettes (Pierce) overnight. les were characterized with a modified Ribogreen assay (Invitrogen) for siRNA entrapment and dynamic light scattering (ZetaPALS, Brookhaven Instruments) for mean particle er. cKK—E12 formulations were made from cholesterol, DSPC, and 00—DMG using a similar method at a molar ratio of 50:10:38.5:l.5. This formulation afforded a le diameter of 60—70 nm with approximately 65% siRNA entrapment.

In Vitro rase Gene Silencing HeLa cells, stably expressing firefly luciferase and Renilla luciferase, were seeded 0 cells/well) into each well of an opaque white 96—well plate(Coming—Costar) and allowed to attach overnight in growth . Growth medium was composed of 90% phenol red—free DMEM, 10% FBS, 100 units/ml penicillin, 100 mg/ml streptomycin rogen). Cells were transfected 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 luciferase expression was analyzed using Dual—Glo assay kits ga). 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 ing experiments. Prior to injection, formulations 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 stered a dose of 0.01 mI/g body—weight. Formulations were administered intravenously via tail vein injection. After 48 or 72 h, body—weight oss was measured and mice were anaesthetized by isofluorane inhalation for blood sample collection by retroorbital eye bleed. Serum was isolated with serum separation 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 s from PBS—injected mice and relative Factor VII expression was determined by comparing treated groups to ted PBS control.

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

The mice mentioned above were systemically injected with formulated 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 n of the adipose tissue and muscle tissue were then removed and imaged. The organs were ed with an Ivis imaging system from Caliper using an excitation wavelength of 675nm and an on wavelength of 720nm. The data were 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 ed. l’lelia cells, stably expressing firetl y lueiferase and a 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 analyzed for lueiferase sion using Dual—file assay kits (Prernega). For visualizatien of cell uptake, eKK-E. 32 was formulated 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 Hoescht. 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 epoxides to produce APPLs. The newly—synthesized single amino acid—based lipid derivatives were evaluated for their capacity to silence hepatic genes in mice. A validated genetic , Factor VII (a blood clotting factor), was selected as a silencing . See, e. g., Akinc, A., et al., A combinatorial library of lipid-like als for ry 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 rticles Enabled by Controlled Microflaidic Formalation. J Am Chem Soc. Formulations that were instable in solution or had no siRNA entrapment were not screened. Stable formulations were injected in mice through systemic stration at a dose of 1 mg/kg (Figure 1). From this initial screening, we identified 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 screened 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. —based dipeptides were reacted with epoxides to give diketopiperizine APPLs. Microwave irradiation was utilized to produce these scaffolds, which dramatically reduced the reaction 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 tic route was developed for the synthesis of cKK- E12 le 2). Diamine 5 was synthesized ing 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 Delineation of Diketopiperazine Self-Assembly Processes: Understanding the Molecular Events ed in N—(Fumaroyl)diketopiperazine ofL-Lys (FDKP) Interactions. Mol. Pharmaceutics, 2008. (2): p. 5), 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. Reactions between lysine—lysine and poly—L—lysine (molecular weight from 500—70000 g/mol) and aldehydes and acrylates were r to those of single amino acids.

The silencing effects were next evaluated. Ten out of 43 compounds 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 ive screening process is an efficient strategy for identifying lead compounds. The s 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 materials were r tested at a lower dose of 0.1 mg/kg. The tail length significantly affects silencing and 12—14 carbon tail lengths appeared favorable 10, —E12, —E14, & — E16). cKK—E12 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 located in the liver at 1 hr and most residual siRNA was cleared by 24 hr h kidney (Figure 2).

Efi‘ects ofApolipoproteins on Cell Uptake and Gene Silencing ] Previous studies have ed that Apolipoprotein E (ApoE) was able to enhance cell uptake and gene ing for a certain type of materials. Akinc, A., et al., Targeted delivery ofRNAi eutics 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, ments were performed with cKK—E12 and ll isoforms of ApoA, ApoB, ApoC, ApoE, and ApoH. Results in Hela cells showed that most apolipoproteins did not affect cell ity with the exception of ApoB. ApoA, ApoC, and ApoH did not show icant effects on silencing compared to free cKK—E12 (Figure 3). However, four different ApoE isoforms significantly improved luciferase silencing.

The activity of cKK—ElZ, 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 on of ApoE3, the order of ing effects was cKK—E12 > 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 ing 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 (Figure 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 s of a group are ered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise t from the context. The invention includes embodiments in which exactly one member of the group is t in, employed in, or ise 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, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is uced into another claim. For example, any claim that is dependent on another 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 elements 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 ments 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 . It is also noted that the terms “comprising” and “containing” are intended to be open and permits the inclusion of additional elements or steps. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise t 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 sub—range 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, l articles, books, manuals, and other publications, all of which are incorporated herein by nce. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular embodiment of the present invention that falls within the prior art may be itly 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 d to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. 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 ed claims. Those of ry skill in the art will appreciate that various changes and modifications to this ption may be made without departing from the spirit or scope of the present ion, as defined in the following claims.

Claims (38)

Claims What is claims is:

1. A compound of Formula (I): or salt thereof; wherein: n is 0 or 1; each instance of m is independently 1; each instance of Z is O; each instance of R1 is independently selected from the group ting of: -H, -CH(CH3)2, -CH(CH3)(CH2CH3), -CH2CH(CH3)2, , , , , , , , , , , , , , , and or is a group of formula (iv): (iv) wherein L is an optionally substituted alkylene; R6 and R7 are each independently a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or a group of the formula (i), provided that at least one instance of R6 and R7 is a group of formula (i); R2 is a group of formula (i); R3 is a group of the a (i); R4 is -ORA4, or -N(RA4)2; wherein each occurrence of RA4 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 nitrogen ting group when attached to a nitrogen atom, or two RA4 groups are joined to form an optionally substituted heterocyclic or optionally substituted aryl ring; R5 is en, or optionally substituted alkyl; and Formula (i) is: wherein formula (i) is selected from formula (i-a) and formula (i-b): (i-a) (i-b) wherein: each instance of R′ is independently hydrogen or optionally substituted alkyl; Y is O, S, NRY, n RY is hydrogen, ally substituted alkyl, ally 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; and RL is C7-12alkyl; wherein “optionally substituted” refers to a carbon atom of a group which may be unsubstituted or independently tuted 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, O2Raa, – 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 membered heteroaryl having ring carbon atoms and 1-4 ring atoms selected from , 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; 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 independently substituted with –OH, –ORaa, Raa, –C(=O)N(Rcc)2, – CO2Raa, –SO2Raa, C1–10 alkyl, C2–10 alkenyl, C2–10 alkynyl, C3–10 yclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and en, C6–14 aryl, and 5–14 membered aryl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, 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, sulfur, and en or 5–14 membered heteroaryl ring having ring carbon atoms and 1-4 ring heteroatoms selected from , sulfur, and nitrogen, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently tuted 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 membered heteroaryl ring having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and en, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently tuted with 0, 1, 2, 3, 4, or 5 Rdd groups; each of Rbb is independently hydrogen, –OH, –ORaa, –N(Rcc)2, –CN, –C(=O)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 yclyl, 3–14 membered heterocyclyl having ring carbon atoms and 1-4 ring heteroatoms ed from oxygen, sulfur, and nitrogen, C6–14 aryl, or 5–14 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms selected 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 atoms selected from oxygen, sulfur, and nitrogen, C6–14 aryl, or 5–14 ed heteroaryl having ring carbon atoms and 1-4 ring atoms 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, carbocyclyl, 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, – 2,–SH, –SRee, , –C(=O)Ree, –CO2H, –CO2Ree, –OC(=O)Ree, –OCO2Ree, – C(=O)N(Rff)2, –OC(=O)N(Rff)2, (=O)Ree, –NRffCO2Ree, –NRffC(=O)N(Rff)2,– NRffSO2Ree, –SO2N(Rff)2, –SO2Ree, –SO2ORee, –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 oxygen, sulfur, and nitrogen, C6–10 aryl, 5–10 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms ed 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 Rgg groups, or two geminal Rdd substituents can be joined to form =O; each of Ree is independently C1–10 alkyl, C2–10 l, C2–10 alkynyl, C3–10 carbocyclyl, C6–10 aryl, 3–10 membered cyclyl having ring carbon atoms and 1-4 ring heteroatoms ed 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, yclyl, heterocyclyl, aryl, and heteroaryl is independently substituted 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 cyclyl having ring carbon atoms and 1-4 ring heteroatoms selected from oxygen, sulfur, and nitrogen, C6–10 aryl and 5–10 membered aryl having ring carbon atoms and 1-4 ring heteroatoms ed from oxygen, sulfur, and nitrogen, or two Rff groups are joined to form a 3–14 ed 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 Rgg groups; each of Rgg is independently halogen, –CN, –NO2, –N3, –SO2H, –SO3H, –OH, –OC1–10 alkyl, 10 alkyl)2, –SH, –SC1–10 alkyl, –SS(C1–10 alkyl), –C(=O)(C1–10 alkyl), –CO2H, – CO2(C1–10 alkyl), –OC(=O)(C1–10 , –OCO2(C1–10 alkyl), –C(=O)NH2, –C(=O)N(C1–10 alkyl)2, –OC(=O)NH(C1–10 alkyl), 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, – SO2OC1–10 alkyl, –OSO2C1–6 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 ed from oxygen, sulfur, and nitrogen, 5–10 membered heteroaryl having ring carbon atoms and 1-4 ring heteroatoms ed from oxygen, sulfur, and en; 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, –C(=O)N(Rcc)2, –CO2Raa, –SO2Raa, –C(=NRcc)Raa, –C(=NRcc)ORaa, – C(=NRcc)N(Rcc)2, –SO2N(Rcc)2, –SO2Rcc, –SO2ORcc, , –C(=S)N(Rcc)2, –C(=O)SRcc, – Rcc, C1–10 alkyl, aralkyl, heteroaralkyl, C2–10 l, 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, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, wherein Raa, Rbb, Rcc and Rdd are as d herein; an oxygen protecting group and a sulfur protecting group are independently selected from the group consisting of –Raa, )2, –C(=O)SRaa, –C(=O)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; provided that when n is 0, R1 is not H.

2. The compound of claim 1, n the group of formula (iv) is of the formula: wherein q is an integer between 1 and 50, inclusive.

3. The compound of claim 1, wherein each instance of R1 is a group of formula (iv).

4. The compound of claim 1, wherein each instance of R5 is hydrogen.

5. The compound of claim 1, wherein the group of formula (i-a) is a group of formula (i-a1) or a group of formula (i-a2): (i-a1) (i-a2).

6. The compound of claim 1, wherein the group of formula (i-b) is a group of formula (i-b1) or a group of a (i-b2): (i-b1) (i-b2)

7. The compound of claim 1, wherein the compound is of Formula (I-f4): (I-f4) or salt thereof.

8. The compound of claim 1, wherein the compound is of Formula (I-f5): (I-f5) or salt thereof.

9. The nd of claim 1, wherein the compound is selected from the group consisting of: , , , , , , and salts thereof.

10. The compound of claim 1, wherein the compound is ed from the group consisting of: , , , , , , , , , , , and salts thereof.

11. A composition comprising a compound of any one of the preceding claims, or salt thereof, and an excipient.

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

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

14. The composition of claim 13, wherein the ition further comprises cholesterol.

15. The composition of claim 13, wherein the composition r comprises a PEGylated lipid.

16. The composition of claim 13, wherein the composition further comprises a phospholipid.

17. The composition of claim 13, wherein the composition further comprises an apolipoprotein.

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

19. The composition of claim 18, wherein the agent is an organic molecule, inorganic molecule, nucleic acid, protein, peptide, polynucleotide, targeting agent, an isotopically d chemical nd, vaccine, an immunological agent, or an agent useful in bioprocessing.

20. The composition of claim 18, wherein the agent is a polynucleotide.

21. The composition of claim 20, wherein the polynucleotide is DNA.

22. The composition of claim 20, wherein the polynucleotide is RNA.

23. The composition of claim 22, n the RNA is RNAi, dsRNA, siRNA, shRNA, miRNA, or antisense RNA.

24. The composition of claim 18, wherein the agent and the compound are not covalently attached.

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

26. The composition of claim 25, wherein the particle is a nanoparticle or microparticle.

27. The composition of claim 25, n the particle is a e, liposome, or lipoplex.

28. The composition of claim 25, wherein the particle encapsulates an agent.

29. A method of screening a compound y, the method comprising: providing a plurality of compounds according to any one of claims 1-10, or salts f; performing at least one assay with the compound library to determine the presence or absence of a desired property; wherein the desired property is solubility in water, solubility at different pH, ability to bind polynucleotides, ability to bind heparin, ability to bind small les, ability to bind protein, ability to form microparticles, ability to increase tranfection efficiency, ability to support cell , ability to support cell attachment, ability to support tissue growth, and/or intracellular delivery of the compound and/or an agent complexed or ed thereto to aid in bioprocessing.

30. A composition for use in treating a e, disorder, or condition from which a subject suffers, comprising a compound according to any one of claims 1-10, or a salt thereof, and an agent.

31. The composition of claim 30, n the disease, disorder, or condition is selected from the group consisting of proliferative disorders, inflammatory disorders, autoimmune disorders, l conditions, liver diseases, and familial amyloid neuropathies.

32. The composition of claim 30, wherein the e, disorder, or condition is a liver disease.

33. The composition of claim 28, wherein the agent is an organic le, inorganic molecule, nucleic acid, protein, peptide, polynucleotide, targeting agent, an isotopically labeled chemical compound, vaccine, or an immunological agent.

34. The composition of claim 33, wherein the agent is a polynucleotide.

35. The composition of claim 34, wherein the polynucleotide is DNA.

36. The composition of claim 34, wherein the polynucleotide is RNA.

37. The composition of claim 36, wherein the RNA carries out RNA interference.

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