US20110200582A1 - Lipids, lipid compositions, and methods of using them - Google Patents

Lipids, lipid compositions, and methods of using them Download PDF

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Publication number
US20110200582A1
US20110200582A1 US12/974,906 US97490610A US2011200582A1 US 20110200582 A1 US20110200582 A1 US 20110200582A1 US 97490610 A US97490610 A US 97490610A US 2011200582 A1 US2011200582 A1 US 2011200582A1
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Prior art keywords
lipid
optionally substituted
composition
group
biologically active
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English (en)
Inventor
Jeremy Baryza
Keith Bowman
Andrew Geall
Tanzina Labonte
Cameron LEE
Chandra Vargeese
Laura WEST
Junping ZHAO
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Novartis AG
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Novartis AG
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Priority to US12/974,906 priority Critical patent/US20110200582A1/en
Assigned to NOVARTIS AG reassignment NOVARTIS AG ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: ZHAO, JUNPING, GEALL, ANDREW, BARYZA, JEREMY, BOWMAN, KEITH, LABONTE, TANZINA, LEE, CAMERON, VARGEESE, CHANDRA, WEST, LAURA
Publication of US20110200582A1 publication Critical patent/US20110200582A1/en
Priority to US14/197,124 priority patent/US9301923B2/en
Abandoned legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/10—Dispersions; Emulsions
    • A61K9/127—Liposomes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/08—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite containing oxygen, e.g. ethers, acetals, ketones, quinones, aldehydes, peroxides
    • A61K47/10—Alcohols; Phenols; Salts thereof, e.g. glycerol; Polyethylene glycols [PEG]; Poloxamers; PEG/POE alkyl ethers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/08—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite containing oxygen, e.g. ethers, acetals, ketones, quinones, aldehydes, peroxides
    • A61K47/14—Esters of carboxylic acids, e.g. fatty acid monoglycerides, medium-chain triglycerides, parabens or PEG fatty acid esters
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/16—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite containing nitrogen, e.g. nitro-, nitroso-, azo-compounds, nitriles, cyanates
    • A61K47/18—Amines; Amides; Ureas; Quaternary ammonium compounds; Amino acids; Oligopeptides having up to five amino acids
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/28—Steroids, e.g. cholesterol, bile acids or glycyrrhetinic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/30—Macromolecular organic or inorganic compounds, e.g. inorganic polyphosphates
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/10—Dispersions; Emulsions
    • A61K9/127—Liposomes
    • A61K9/1271—Non-conventional liposomes, e.g. PEGylated liposomes, liposomes coated with polymers
    • A61K9/1272—Non-conventional liposomes, e.g. PEGylated liposomes, liposomes coated with polymers with substantial amounts of non-phosphatidyl, i.e. non-acylglycerophosphate, surfactants as bilayer-forming substances, e.g. cationic lipids
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07J—STEROIDS
    • C07J41/00—Normal steroids containing one or more nitrogen atoms not belonging to a hetero ring
    • C07J41/0033—Normal steroids containing one or more nitrogen atoms not belonging to a hetero ring not covered by C07J41/0005
    • C07J41/0055—Normal steroids containing one or more nitrogen atoms not belonging to a hetero ring not covered by C07J41/0005 the 17-beta position being substituted by an uninterrupted chain of at least three carbon atoms which may or may not be branched, e.g. cholane or cholestane derivatives, optionally cyclised, e.g. 17-beta-phenyl or 17-beta-furyl derivatives
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07J—STEROIDS
    • C07J43/00—Normal steroids having a nitrogen-containing hetero ring spiro-condensed or not condensed with the cyclopenta(a)hydrophenanthrene skeleton
    • C07J43/003—Normal steroids having a nitrogen-containing hetero ring spiro-condensed or not condensed with the cyclopenta(a)hydrophenanthrene skeleton not condensed
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07J—STEROIDS
    • C07J9/00—Normal steroids containing carbon, hydrogen, halogen or oxygen substituted in position 17 beta by a chain of more than two carbon atoms, e.g. cholane, cholestane, coprostane
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2300/00—Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07J—STEROIDS
    • C07J31/00—Normal steroids containing one or more sulfur atoms not belonging to a hetero ring
    • C07J31/006—Normal steroids containing one or more sulfur atoms not belonging to a hetero ring not covered by C07J31/003

Definitions

  • This invention relates to cationic lipid compounds, stealth lipid compounds and to compositions comprising such compounds.
  • the invention also relates to processes for making such compounds and compositions, and to methods and uses of such compounds and compositions, e.g., to deliver biologically active agents to cells and tissues.
  • the invention describes optimized pKa ranges for cationic lipids for use in lipid formulations to deliver biologically active agents to specific cell types, including especially liver and tumors, and methods for optimizing the formulations.
  • biologically active agents including therapeutically relevant compounds
  • the delivery of biologically active agents to subjects is often hindered by difficulties in the compounds reaching the target cell or tissue.
  • trafficking of many biologically active agents into living cells is highly restricted by the complex membrane systems of the cells. These restrictions can result in the need to use much higher concentrations of biologically active agents than is desirable to achieve a result, which increases the risk of toxic effects and side effects.
  • One solution to this problem is to utilise specific carrier molecules which are allowed selective entry into the cell. Lipid carriers, biodegradable polymers and various conjugate systems can be used to improve delivery of biologically active agents to cells.
  • nucleic acids are stable for only a limited duration in cells or plasma.
  • RNA interference RNAi therapy
  • RNA drugs antisense therapy and gene therapy, among others, has increased the need for effective means of introducing active nucleic acid agents into cells.
  • compositions that can stabilise and deliver nucleic acid-based agents into cells are of particular interest.
  • Viral vectors can be used to transfer genes efficiently into some cell types, but they generally cannot be used to introduce chemically synthesized molecules into cells.
  • compositions incorporating cationic lipids which interact with a biologically active agent at one part and interact with a membrane system at another part (for a review, see Feigner, 1990, Advanced Drug Delivery Reviews, 5, 162-187 and Feigner, 1993, J. Liposome Res., 3, 3-16). Such compositions are reported to contain liposomes.
  • Liposomes are attractive carriers since they protect biological molecules from degradation while improving their cellular uptake.
  • liposomes which contain cationic lipids are commonly used for delivering polyanions (e.g. nucleic acids).
  • polyanions e.g. nucleic acids
  • Such liposomes can be formed using cationic lipids alone and optionally including other lipids and amphiphiles such as phosphatidylethanolamine. It is well known in the art that both the composition of the lipid formulation as well as its method of preparation affect the structure and size of the resultant aggregate.
  • cationic lipids for cellular delivery of biologically active agents has several advantages.
  • the encapsulation of anionic compounds using cationic lipids is essentially quantitative due to electrostatic interaction.
  • the cationic lipids interact with the negatively charged cell membranes initiating cellular membrane transport (Akhtar et al., 1992, Trends Cell Bio., 2, 139; Xu et al., 1996, Biochemistry 35, 5616).
  • cationic lipid compounds generally consist of two alkyl or alkenyl chains linked to the nitrogen containing “head” group.
  • R 3 , R 4 and R 5 taken together being quinuclidino, piperidino, pyrrolidino or morpholino.
  • WO 2005/121348 discloses lipid-based formulations.
  • the nucleic acid-lipid particles disclosed therein comprise an interference RNA molecule, a cationic lipid with alkyl side chains from about 10 to 20 carbon atoms having more than a single site of unsaturation, a noncationic lipid and a conjugated lipid that inhibits aggregation of the particle such as a polyethyleneglycol (PEG)-lipid conjugate or a polyamide (ATTA)-conjugate.
  • PEG polyethyleneglycol
  • ATTA polyamide
  • Specific cationic lipid compounds disclosed in this patent application include DSDMA, DODMA, DLinDMA, DLenDMA.
  • liposomes which comprise amino lipids such as the following.
  • US 2006/0240554 and related applications US 2008/0020058 and US 2009/0048197 also relate to cationic lipids. These lipids are reported to be capable of delivering biologically active agents, including small nucleic acid molecules such as short interfering nucleic acids (siNA) to cells and/or tissues.
  • small nucleic acid molecules such as short interfering nucleic acids (siNA)
  • WO2009/086558 discloses the following compounds:
  • amino lipids having the following general formula (In which R 3 and R 4 may join to form an optionally substituted heterocyclic ring of 4 to 6 carbon atoms and 1 or 2 heteroatoms chosen from nitrogen and oxygen):
  • the invention provides novel cationic lipids and stealth lipids, and formulations containing them, and their methods of use. Also provided are formulations for use of such lipids for delivery of therapeutically effective amounts of drugs, including especially RNAi constructs, for delivery to subject in need thereof. Particular formulations containing cationic lipids with a pKa within specific ranges are provided for administering therapeutically effective amounts of drugs to the liver and/or to tumor in the somatic tissues of a subject.
  • formulations that are the most effective for delivery to tumors contain cationic lipids with a pKa of about 6.1 or below, although particular ranges include from about 5.0 to about 6.7, including especially from about 5.2 to about 6.3, or from about 5.4 to about 6.2, or from about 5.8 to about 6.1, depending on tumor type; whereas formulations that are the most effective for delivery to liver (as described in greater detail below) contain cationic lipids with a pKa of about 6.1 or above, although particular ranges include from about 5.1 to about 7.4, including from about 5.3 to about 7.3, and including especially from about 5.9 to about 7.0, and in one embodiment is from about 6.2 to about 6.8.
  • Formulations may be further optimized by one skilled in the art by adjusting other aspects of the formulation, including but not limited to individual selection of, e.g., the pKa of the cationic lipid optimized for the type of cell or organ being targeted, the cationic lipid used, the stealth lipid used, the helper lipid, the neutral lipid used, including whether the neutral lipid is present or absent, the ratio of the selected helper lipid, optional neutral lipid, stealth lipid and cationic lipid, the N/P ratio, the particle size, the dosage regimen, the dose given, the formulation method, and the like.
  • This invention provides cationic lipids (also referred to herein as “compounds”) and compositions comprising such lipids.
  • the invention also provides processes for making such compounds and compositions, and methods and uses of such compounds and compositions to deliver biologically active (including therapeutic) agents to cells (including in vivo delivery) and for optimizing such formulations for delivery in vivo to specific cell types and tissues.
  • This invention also provides stealth lipids.
  • the invention provides a compound of formula (I):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is absent or optionally substituted C 1-4 alkylene
  • b is absent or optionally substituted C 1-4 alkylene
  • c is absent or optionally substituted C 1-4 alkylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is absent or -(L a ) d -(L b ) e -(L c ) f -, wherein
  • Y 2 is an optionally substituted steroid.
  • the present invention also provides a pharmaceutical composition
  • a pharmaceutical composition comprising a compound of formula (I).
  • These compositions may comprise a biologically active agent, optionally in combination with other lipid components.
  • the present invention also provides a pharmaceutical composition comprising a compound of formula (XI).
  • These compositions may comprise a biologically active agent, optionally in combination with other lipid components.
  • the invention provides a compound of formula (XI):
  • Z is a hydrophilic head group component selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(N-vinyl pyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein the polymer may be linear or branched, and wherein the polymer may be optionally substituted;
  • n is a number-averaged degree of polymerization between 10 and 200 units of Z, wherein n is optimized for different polymer types;
  • L 1 is an optionally substituted C 1-10 alkylene or C 1-10 heteroalkylene linker including zero, one, two or more of an ether (e.g., —O—), ester (e.g., —C(O)O—), succinate (e.g., —O(O)C—CH 2 —CH 2 —C(O)O—)), carbamate (e.g., —OC(O)—NR′—), carbonate (e.g., —OC(O)O—), ketone (e.g., —C—C(O)—C—); carbonyl (e.g., —C(O)—); urea (e.g., —NRC(O)NR′—), amine (e.g., —NR′—), amide (e.g., —C(O)NR′—), imine (e.g., —C(NR′)—), thioether (e.g., —S—
  • R′ is independently selected from —H, —NH—, —NH 2 , —O—, —S—, a phosphate or an optionally substituted C 1-10 alkylene;
  • X 1 and X 2 are independently selected from a carbon or a heteroatom selected from —NH—, —O—, —S— or a phosphate;
  • a 1 and A 2 are independently selected from a C 6-30 alkyl, C 6-30 alkenyl, and C 6-30 alkynyl, wherein A 1 and A 2 may be the same or different,
  • compositions containing lipids of the invention are useful, e.g., in delivering therapeutic compounds (e.g., one or more biologically active agents) for the treatment of disorders or diseases, including especially those disorders or diseases that respond to modulation of gene expression in a patient or administration of a therapeutic to a targeted cell or tissue.
  • therapeutic compounds e.g., one or more biologically active agents
  • the compounds and compositions of the present invention can be used to treat diseases and conditions in a patient.
  • the compounds can be utilised in liposomes and/or lipid nanoparticle formulation compositions to deliver biologically active agents, including, e.g., antibodies, low molecular weight compositions, protein therapeutics and nucleic acid compositions such as siRNA for RNAi, to cells or tissues.
  • the biologically active agents are delivered, utilising the described cationic lipids, to cells, during which process they may crass epithelial and endothelial tissues, such as skin, mucous membranes, vascular tissues, gastrointestinal tissues, blood brain barrier tissues, opthalmological tissues, pulmonary tissues, liver tissues, cardiac tissues, kidney tissues, tumor tissues, etc.
  • the compounds and compositions can be used for both local and systemic delivery of the biologically active agents.
  • RNAi therapeutics have some effectiveness when directed to tissues in the eye, skin, lungs and liver.
  • a need remains for compositions and methods for delivery of therapeutically effective amounts of RNAi for the treatment of all other somatic tissues and for cancer, including metastatic cancers.
  • formulations with the most effective lipids for delivery to tumors contain cationic lipids with a pKa of from about 5.0 to about 6.7, including especially from about 5.8 to about 6.1, depending on tumor type, whereas formulations with the most effective lipids for delivery to liver (as described in greater detail below) contain cationic lipids with a pKa of from about 5.1 to about 7.4, including especially from about 5.9 to about 7.0.
  • a cationic lipid with a pKa of about 6.1 or below is more effective in a formulation for delivery of a biologically active agent to a tumor or tumor cell; whereas a cationic lipid with a pKa of about 6.1 or above is more effective in a formulation for delivery of a biologically active agent to the liver or a liver cell.
  • novel cationic lipids are described, wherein formulations containing these cationic lipids may deliver therapeutically effective amounts of RNAi compositions to tumors when administered to a subject in vivo.
  • formulations containing these cationic lipids may deliver therapeutically effective amounts of RNAi compositions to liver when administered to a subject in vivo.
  • the invention provides a compound of formula (I):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is absent or optionally substituted C 1-4 alkylene
  • b is absent or optionally substituted C 1-4 alkylene
  • c is absent or optionally substituted C 1-4 alkylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is absent or -(L a ) d -(L b ) e -(L c ) f -, wherein
  • Y 2 is an optionally substituted steroid.
  • a is an optionally substituted C 1-2 alkylene. In one embodiment of formula I, a is an optionally substituted C 1 alkylene. In one embodiment of formula I, b is an optionally substituted C 0-2 alkylene. In one embodiment of formula I, b is an optionally substituted C 1 alkylene. In one embodiment of formula I, c is absent or is an optionally substituted C 1 alkylene. In one embodiment of formula I, a, b and c are unsubstituted. In one embodiment of formula I, c is absent.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl or C 3-20 -heterocycloalkynyl group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 5-16 group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 5-12 group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 5 group, C 6 group or C 7 group. In one embodiment of formula I, R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 5 group or C 6 group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached are selected from H 1 to H 52 .
  • X 1 is O. In one embodiment of formula I, X 2 is O.
  • L comprises at least one heteroatom. In one embodiment of formula I, L comprises at least one O atom. In one embodiment of formula I, L comprises at least two heteroatoms. In one embodiment of formula I, L comprises at least two substitutions of O atoms. In one embodiment of formula I, L c is an optionally substituted C 1-15 alkylene or C 1-15 heteroalkylene. In one embodiment of formula I, L c is selected from any one or more of formulae to L c-i to L c-xxxxiii .
  • L c is an optionally substituted C 1-15 heteroalkylene. In one embodiment of formula I, L c is an optionally substituted C 1-11 group. In one embodiment of formula I, L c is an optionally substituted C 1-9 group. In one embodiment of formula I, L c is an optionally substituted C 3-8 group. In one embodiment of formula I, L c is an optionally substituted C 4-7 group. In one embodiment of formula I, L c is an optionally substituted C 5 , C 6 or C 7 group.
  • Y 1 is a C 12-28 group. In one embodiment of formula I, Y 1 is a C 14-26 group. In one embodiment of formula I, Y 1 is a C 16-24 group. In one embodiment of formula I, Y 1 is a C 16-22 group. In one embodiment of formula I, Y 1 has at least one alkene group. In one embodiment of formula I, Y 1 has 1, 2 or 3 alkene groups. In one embodiment of formula I, Y 1 has an alkene group at the omega-3 position. In one embodiment of formula I, Y 1 has an alkene group at the omega-6 position. In one embodiment of formula I, Y 1 has an alkene group at the omega-9 position.
  • Y 1 has at least one cis unsaturated alkene group. In one embodiment of formula I, Y 1 has at least two cis unsaturated alkene groups. In one embodiment of formula I, Y 1 has at least three cis unsaturated alkene groups. In one embodiment of formula I, Y 1 is selected from to
  • Y 2 is linked to L via an oxygen atom on the optionally substituted steroid. In one embodiment of formula I, Y 2 is linked to L via an oxygen atom on the 3-position of the A steroid ring. In one embodiment of formula I, Y 2 is a sterol in which the hydrogen atom of the hydroxy group at the 3-position of the A steroid ring has been removed. In one embodiment of formula I, the sterol is cholesterol.
  • a second embodiment of the invention is represented by a compound of formula (II):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is absent or optionally substituted C 1-4 alkylene
  • b is absent or optionally substituted C 1-4 alkylene
  • c is absent or optionally substituted C 1-4 alkylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is -(L a ) d -(L b ) e -(L c ) f -, wherein
  • L comprises one or more heteroatoms
  • Y 2 is an optionally substituted steroid.
  • a third embodiment of the invention is represented by a compound of formula (III):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is -(L a ) d -(L b ) e -(L c ) f -, wherein
  • Y 2 is an optionally substituted steroid.
  • a fourth embodiment of the invention is represented by a compound of formula (IV):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is -(L a ) d -(L b ) e -(L c ) f -, wherein
  • L comprises one or more heteroatoms
  • a fifth embodiment of the invention is represented by a compound of formula (V):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O
  • X 2 is O
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is -(L a ) d -(L b ) e -(L c ) f -, wherein
  • L comprises one or more heteroatoms
  • a sixth embodiment of the invention is represented by a compound of formula (VI):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O
  • X 2 is O
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • Y 2 is an optionally substituted steroid.
  • a seventh embodiment of the invention is represented by a compound of formula (VII):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O
  • X 2 is O
  • Y 1 is an optionally substituted C 16-22 alkenyl group
  • Y 2 is an optionally substituted steroid.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O
  • X 2 is O
  • Y 1 is an optionally substituted C 16-22 alkenyl group
  • Y 2 is cholesterol connected through the hydroxy group at the 3-position of the A steroid ring, the hydrogen atom of said hydroxy group being absent.
  • a ninth embodiment of the invention is represented by a compound of formula (IX):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is -(L a ) d -(L b ) e -(L c ) f -, wherein
  • L comprises one or more heteroatoms
  • a tenth embodiment of the invention is represented by a compound of formula (X):
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group;
  • a is methylene
  • X 1 is O or S
  • X 2 is O or S
  • Y 1 is optionally substituted C 10-30 alkenyl, C 10-30 alkynyl, C 10-30 heteroalkenyl or C 10-30 heteroalkynyl;
  • L is -(L a ) d -(L b ) e -(L b ) f -, wherein
  • L comprises one or more heteroatoms
  • stealth lipids containing a hydrophilic head group linked to a lipid moiety. Further characterization of stealth lipids is provided below.
  • Z is a hydrophilic head group component selected from PEG and polymers based on poly(oxazoline), poly(ethyleneoxide), poly(vinyl alcohol), poly(glycerol), poly(N-vinylpyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein the polymer may be linear or branched, and wherein the polymer may be optionally substituted;
  • n is a number-averaged degree of polymerization between 10 and 200 units of Z, wherein n is optimized for different polymer types;
  • L 1 is an optionally substituted C 1-10 alkylene or C 1-10 heteroalkylene linker including zero, one, two or more of an ether (e.g., —O—), ester (e.g., —C(O)O—), succinate (e.g., —O(O)C—CH 2 —CH 2 —C(O)O—)), carbamate (e.g., —OC(O)—NR′—), carbonate (e.g., —OC(O)O—), ketone (e.g., —C—C(O)—C—), carbonyl (e.g., —C(O)—), urea (e.g., —NRC(O)NR′—), amine (e.g., —NR′—), amide (e.g., —C(O)NR′—), imine (e.g., —C(NR′)—), thioether (e.g., —S—
  • R′ is independently selected from —H, —NH—, —NH 2 , —O—, —S—, a phosphate or an optionally substituted C 1-10 alkylene;
  • X 1 and X 2 are independently selected from a carbon or a heteroatom selected from —NH—, —O—, —S— or a phosphate;
  • a 1 and A 2 are independently selected from a C 6-30 alkyl, C 6-30 alkenyl, and C 6-30 alkynyl, wherein A 1 and A 2 may be the same or different,
  • the invention provides a stealth lipid of formula (XII)
  • PEG is a polyethylene glycol) subunit, wherein the PEG may be linear or branched;
  • n is a number-averaged degree of polymerization between 10 and 200 units of PEG, preferably about 23 units, about 45 units or about 68 units;
  • L 1 is an optionally substituted C 1-10 alkylene or C 1-10 heteroalkylene linker containing one, two or more of an ether, ester, succinate, carbamate, carbonate, ketone, carbonyl, urea, amine, amide, imine, thioether, xanthate, and phosphodiester; any of which may be substituted by zero, one or more PEG groups;
  • X 1 and X 2 are independently selected from carbon or oxygen;
  • a 1 and A 2 are independently selected from a C 6-30 alkyl, C 6-30 alkenyl, and C 6-30 alkynyl, wherein A 1 and A 2 may be the same or different,
  • lipid nanoparticles formulated using the same process and with otherwise identical compositions, but differing in the stealth lipids are delivered to the liver.
  • the lipid nanoparticle containing the prior art stealth lipid S010 and delivering an siRNA construct specific to factor VII (“FVII”) demonstrates an in vivo inhibition of 72.2% when administered to the liver, while the lipid nanoparticle containing the stealth lipid S006 in comparison demonstrated an in vivo Factor VII inhibition of 83.8%.
  • lipid nanoparticles with otherwise identical compositions except for the PEG/stealth lipid are compared for effective delivery of an siRNA specific to Polo-Like Kinase 1 (“PLK1”).
  • the lipid nanoparticle containing the prior art stealth lipid S011 demonstrates an in vivo PLK1 inhibition of 46% in the tumor tissue, while lipid nanoparticles containing the stealth lipids S004, S007, S009, S008, and S005 demonstrate in vivo PLK1 inhibitions of 56%, 65%, 64%, 60%, and 52%, respectively, in the tumor tissue.
  • the stealth lipids S001 through S009 and S012 through S026 individually and as a class thereby demonstrate improved characteristics when used in formulations and therapeutic composition for use in delivery of biologically active agents, in this case for one or more siRNA.
  • Novel stealth lipids are provided in the invention.
  • the stealth lipid is S001.
  • the stealth lipid is S002.
  • the stealth lipid is S003.
  • the stealth lipid is S004.
  • the stealth lipid is S005.
  • the stealth lipid is S006.
  • the stealth lipid is S007.
  • the stealth lipid is S008.
  • the stealth lipid is S009.
  • the stealth lipid is S012.
  • the stealth lipid is S013.
  • the stealth lipid is S014.
  • the stealth lipid is S015.
  • the stealth lipid is S016. In one embodiment, the stealth lipid is S017. In one embodiment, the stealth lipid is S018. In one embodiment, the stealth lipid is S019. In one embodiment, the stealth lipid is S020. In one embodiment, the stealth lipid is S021. In one embodiment, the stealth lipid is S022. In one embodiment, the stealth lipid is S023. In one embodiment, the stealth lipid is S024. In one embodiment, the stealth lipid is S025. In one embodiment, the stealth lipid is S026.
  • lipid formulations for delivery of biologically active agents can be adjusted to preferrentially target one cell type or organ over another by alterring only the cationic lipid included in the formulations.
  • cationic lipids whose pKa is about 6.1 or above are much more effective in formulations targeting the liver compared to formulations containing cationic lipids whose pKa is about 6.1 or lower, which are comparatively more effective in formulation targeting tumors in vivo.
  • formulations with the most effective lipids for delivery to tumors contain cationic lipids with a pKa of from about 5.0 to about 6.7, including especially from about 5.2 to about 6.3, or from about 5.4 to about 6.2, or from about 5.8 to about 6.1, depending on tumor type; whereas formulations with the most effective lipids for delivery to liver (as described in greater detail below) contain cationic lipids with a pKa of from about 5.1 to about 7.4, including from about 5.3 to about 7.3, including from about 5.9 to about 7.0, and in one embodiment including from about 6.2 to about 6.8.
  • cationic lipids with the desired pKa range, stealth lipids, helper lipid, optional alkyl resorcinol based lipids and optional neutral lipids into formulations, including, e.g., liposome formulations, liponanoparticle (LNP) formulations, and the like for delivery to specific cells and tissues in vivo.
  • further optimization is obtained by adjusting the lipid molar ratio between these varioustypes of lipids.
  • further optimization is obtained by adjusting one or more of: the desired particle size, N/P ratio, formulation methods and/or dosing regimen (e.g., number of doses administered over time, actual dose in mg/kg, timing of the doses, combinations with other therapeutics, etc.).
  • formulation methods and/or dosing regimen e.g., number of doses administered over time, actual dose in mg/kg, timing of the doses, combinations with other therapeutics, etc.
  • cationic lipids of the invention are provided wherein formulation for delivery of therapeutically effective amounts of biologically active agents comprise at least one each of a cationic lipid, a helper lipid, and a stealth lipid. In one embodiment, such a formulation further comprises at least one neutral lipid. In one embodiment the formulation is optimized for delivery of a biologically active agent for delivery to a tumor. In one embodiment the formulation is optimized for delivery of a biologically active agent for delivery to liver. In one embodiment the formulation is optimized for delivery of a particular type of biologically active agent.
  • biologically active agents include, but are not limited to, e.g., antibodies, cholesterol, hormones, antivirals, peptides, polypeptides, proteins, nucleoproteins, chemotherapeutics, low molecular weight drugs, vitamins, co-factors, nucleosides, nucleoside derivatives, nucleotides, oligonucleotides, enzymatic nucleic acids, antisense nucleic acids, triplex forming oligonucleotides, 2,5-A antisense chimeras, allozymes, aptamers, ribozyme, decoy RNA molecules and analogs thereof, and small nucleic acid molecules, such as short interfering nucleic acid (siRNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA).
  • Such biologically active agents may be optionally optimized with one or more further chemical and biologic agents to increase
  • preferred formulations are selected from those that deliver sufficient amounts of a biologically active agent to effectively modulate the activity of the therapeutic target in a subject in need of such administration.
  • an effective amount of an RNAi, siRNA, siNA, or shRNA is the amount that provides a knock down (KD) at least 20% or greater, 50% or greater, 60% or greater, 70% or greater, 75% or greater, 80% or greater, 85% or greater, 90% or greater, 95% or greater, or up to 100% of the target mRNA expressed in the target cell.
  • KD knock down
  • choice of which therapeutically relevant KD range is needed for effective treatment may vary by the pathway being targetted, by cell type or tissue, and/or by the disease or disorder being treated.
  • Cationic lipids of the type described above, wherein R 1 and R 2 together with the nitrogen atom to which they are attached form a cyclic “headgroup”, are reported herein to be effective cationic lipids for use in lipid formulations. Furthermore, it is now reported that the presence of the cyclic headgroup unexpectedly alters the behaviour of a lipid formulation and, in particular, that it changes the influence of the other substituents.
  • the headgroup (i.e., R 1 —N—R 2 ) of the cationic lipid compounds of the invention contains a tertiary amine group. This feature causes the compounds to behave differently, e.g., from if they had, e.g., quaternary (cationic) amine groups because quaternization of the nitrogen puts a fixed charge on the atom, removing its pH responsiveness and causing a compound to behave very differently.
  • inventive compounds E0027 and E0014 altered the ability of the cationic lipid as a whole to act as an effective delivery agent in a formulation as compared to lipids E0173 and E0172, which differs only in the head group.
  • a formulation containing a particular cationic lipid (E0173, CLinDMA) with the —N(Me) 2 headgroup when used in a formulation for delivery of an RNAi construct specific to Factor VII, demonstrates an in vivo Factor VII inhibition of 98.5%.
  • the activity of the compound (E0172) is found to decrease: an in vivo Factor VII inhibition of 40.8% is found.
  • one embodiment of the invention comprises those compounds wherein L comprises one or more heteroatoms.
  • L comprises one or more heteroatoms.
  • the skilled person would not arrive at such compounds starting from the disclosure of CLinDMA because, as noted above, the skilled person starting from compounds with a CLinDMA headgroup would have discovered that an L group comprising two or more heteroatoms reduces the efficacy of the final compounds, and so would not have provided a compound which comprises such a group.
  • the efficacy of the lipid formulations of the invention is related to pKa.
  • the pKa of a cationic lipid can be adjusted by altering the structure, e.g. by varying the number of heteroatoms in L or by varying the nature of the headgroup.
  • the most effective cationic lipids for use in such formulations have a pKa of from about 5.1 to about 7.4.
  • cationic lipids with a pKa of from about 5.3 to about 7.3 are provided for formulation of this invention for liver delivery.
  • cationic lipids with a pKa of from about 5.9 to about 7.0 are provided for formulation of this invention for liver delivery.
  • preferred lipids have a pKa range of about 6.2 to about 6.8 for use in formulation for delivery of biologically active agents to the liver.
  • a surprising discovery of the invention is that tumor tissues have different optimal pKa ranges for efficacy.
  • the pKa ranges in the previous paragraph apply to the extent that the lipids are intended to deliver biologically active agents to liver cells.
  • the most effective cationic lipids of the invention for use in such formulations have a pKa of from about 5.0 to about 6.7, and thus are preferred lipids for delivery to tumors in one embodiment.
  • cationic lipids with a pKa of from about 5.0 to about 6.7 are provided for formulation of this invention for use in delivery of biologically active agents to one or more tumors.
  • cationic lipids with a pKa of from about 5.2 to about 6.3 are provided for formulation of this invention for use in delivery of biologically active agents to one or or more tumors.
  • cationic lipids with a pKa of from about 5.4 to about 6.2 are provided for formulation of this invention for use in delivery of biologically active agents to one or or more tumors.
  • cationic lipids with a pKa of from about 5.8 to about 6.1 are provided for formulation of this invention for use in delivery of biologically active agents to one or or more tumors.
  • the cationic lipid used in the formulation has a pKa optimized for delivery of a biologically active agent to a particular tumor or cell type.
  • Tumor types may be primary tumors or may be metastatic.
  • formulations optimized for delivery to Hep3B-like tumors contain cationic lipids with a pKa of from about 5.0 to about 6.7. In one specific embodiment, formulations optimized for delivery to Hep3B-like tumors contain cationic lipids with a pKa of from about 5.3 to about 6.3. In one specific embodiment, formulations optimized for delivery to Hep3B-like tumors contain cationic lipids with a pKa of from about 5.4 to about 5.9. In one specific embodiment, formulations optimized for delivery to Hep3B-like tumors contain cationic lipids with a pKa of from about 5.8 to about 5.9.
  • formulations optimized for delivery to HepG2-like tumors contain cationic lipids with a pKa of from about 5.2 to about 6.2. In one specific embodiment, formulations optimized for delivery to Hep3B-like tumors contain cationic lipids with a pKa of from about 5.3 to about 6.2. In one specific embodiment, formulations optimized for delivery to Hep3B-like tumors contain cationic lipids with a pKa of from about 5.6 to about 6.1. In one specific embodiment, formulations optimized for delivery to HepG2-like tumors contain cationic lipids with a pKa of about 6.1.
  • formulations optimized for delivery to 786-O-like renal tumors, or their metastases contain cationic lipids with a pKa of about 6.1.
  • lipid pKa ranges it is reasonable to postulate that other tissues, indications, tumor types or administration routes may possess preferred lipid pKa ranges.
  • various tissues, indications, tumor types or administration routes may possess preferred cationic lipid pKa ranges, N/P ratios, particle size, cationic lipid used, stealth lipid used, helper lipid used, optional use of a selected neutral lipid, relative molar ratios of each lipid component, formulation method, biologically active agent to be delivered, and dosage regimen including dose given. Optimizing each of these aspects, either independently or in a coordinated manner, is described below, and many specific aspects of such optimization is believed to be within the ability of one skilled in the art without requiring undue experimentation.
  • Formulations may be optimized by one skilled in the art by adjusting other aspects of the formulation, including but not limited to individual selection of, e.g., the pKa of the cationic lipid optimized for the type of cell or organ being targeted; the cationic lipid used; the stealth lipid used; the helper lipid used; whether a neutral lipid is present or absent; the choice of neutral lipid used if present; the molar ratio of the selected helper lipid, optional neutral lipid, stealth lipid and cationic lipid; the N/P ratio; the particle size; the dosage regimen; the dose given; the formulation method; and the like.
  • a is optionally substituted C 1-2 alkylene. In one embodiment, a is optionally substituted C 1 alkylene.
  • b is optionally substituted C 0-2 alkylene. In one embodiment, b is optionally substituted C 1 alkylene.
  • c is absent or is optionally substituted C 1 alkylene. In one embodiment, c is absent.
  • a, b and c are, if present, unsubstituted.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl group, C 5 -heteroaryl or C 6 -heteroaryl group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl or C 3-20 -heterocycloalkynyl group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted C 3-20 -heterocycloalkyl group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted cyclic C 5-16 group. In one embodiment, R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted cyclic C 5-12 group. In one embodiment, R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted cyclic C 5 group, cyclic C 6 group or cyclic C 7 group. In one embodiment, R 1 and R 2 together with the nitrogen atom to which they are attached form an optionally substituted cyclic C 5 group or cyclic C 6 group.
  • R 1 and R 2 together with the nitrogen atom to which they are attached forms a cyclic species which comprises at least one oxygen atom.
  • R 1 and R 2 together with the nitrogen atom to which they are attached are selected from at least one of the headgroups H 1 to H 52 as provided in Table 1.
  • cationic lipids herein with pKa ranges in the desired range are preferred, including especially for formulations for delivery of biologically active agents.
  • a cationic lipid with a pKa of from about 5.1 to about 7.4 are generally effective when used in a formulation for targetting liver.
  • the pKa of a cationic lipid is from about 5.1 to about 7.4 for delivery to liver.
  • a cationic lipid with a pKa from about 5.3 to about 7.3 for use in formulations specific for targeting the liver.
  • the pKa of a cationic lipid is from about 5.3 to about 7.3 for delivery to liver.
  • the pKa of a cationic lipid is from about 5.9 to about 7.0 for delivery to liver.
  • the pKa of the cationic lipid is from about 6.2 to about 6.8 for delivery to liver.
  • a cationic lipid with a pKa of from about 5.0 to about 6.7 is particularly effective when used in a formulation for delivery of a biologically active agent to a tumor.
  • the pKa of a cationic lipid is from about 5.0 to about 6.7 for delivery to tumors.
  • the pKa of a cationic lipid is from about 5.2 to about 6.3 for delivery to tumors.
  • the pKa of a cationic lipid is from about 5.4 to about 6.2 for delivery to tumors.
  • the pKa of the cationic lipid is from about 5.8 to about 6.1 for delivery to tumors.
  • the pKa of a cationic lipid is from about 6.1 or below for delivery of a biologically active agent to a tumor or tumor cell.
  • the pKa of the cationic lipid for use in a formulation for delivery of a biologically active agent may be further optimized depending on tumor type. For example, as provided in Tables 9, 10 and 11, RNAi constructs specific to PLK1 mRNA are differentially delivered to Hep3B, HepG2 and 786-0 renal tumors injected into the flank of a mouse, in a manner that correlates with the pKa of the cationic lipid in the LNP formulation.
  • the optimal pKa range for knockdown of PLK1 in Hep3B tumors in vivo differs from the optimal pKa range for HepG2 and 786-0 tumors, although both ranges fall within the general range of 5.0 to 6.7 as listed in the above paragraph, and all ranges in general include cationic lipids with a lower pKa than is optimal for delivery to liver.
  • the cationic lipids of the invention have pKa ranges from about 5.0 to about 6.7. In one embodiment, the pKa of a cationic lipid is from about 5.3 to about 6.3 for delivery to Hep3B-like tumors. In one embodiment, the pKa of a cationic lipid is from about 5.4 to about 5.9 for delivery to Hep3B-like tumors. In one embodiment, the pKa of a cationic lipid is from about 5.8 to about 5.9 for delivery to Hep3B-like tumors.
  • the cationic lipids of the invention have pKa ranges from about 5.2 to about 6.2. In one embodiment, the pKa of a cationic lipid is from about 5.3 to about 6.2 for delivery to HepG2-like tumors. In one embodiment, the pKa of a cationic lipid is from about 5.6 to about 6.1 for delivery to HepG2-like tumors. In one embodiment, the pKa of a cationic lipid is about 6.1 to HepG2-like tumors or to 786-0 renal tumor-like tumors.
  • X 1 is O. In another embodiment, X 2 is O. In one embodiment, both X 1 and X 2 are O.
  • L comprises at least one heteroatom. This means that the chain which provides a direct link between X 2 and Y 2 has at least one heteroatom. In other words, any heteroatom in a substituent on L does not count for these purposes. In one embodiment, L comprises at least one O atom.
  • L comprises at least two heteroatoms. In one embodiment, L comprises at least two O atoms.
  • L c is optionally substituted C 1-15 alkylene or C 1-15 heteroalkylene. In one embodiment, L c is optionally substituted C 1-15 alkylene or C 1-15 heteroalkylene and d and e are both zero (0).
  • L c is selected from one of formulae L c-i to L c-xxxxiii . In one embodiment, L c is selected from one of formulae L c-i to L c-xxxxiii and d and e are both zero (0).
  • L c is preferably selected from L c-i , L c-iv to L c-vii and L c-ix to L c-xxxxiii .
  • L c is optionally substituted C 1-15 heteroalkylene.
  • L c is an optionally substituted C 1-11 group. In one embodiment, L c is an optionally substituted C 1-9 group. In one embodiment, L c is an optionally substituted C 3-8 group. In one embodiment, wherein L c is an optionally substituted C 4-7 group. In one embodiment, L c is an optionally substituted C 5 , C 6 or C 7 group.
  • Y 1 is a C 12-28 group. In one embodiment, Y 1 is an optionally substituted C 14-26 group. In one embodiment, Y 1 is an optionally substituted C 16-24 group. In one embodiment, Y 1 is an optionally substituted C 16-22 group. In one embodiment, the optionally substituted Y 1 chain is 18, 19, 20 or 21 atoms long.
  • Y 1 is preferably alkenyl or heteroalkenyl.
  • Y 1 has at least one alkene group. In one embodiment, Y 1 has 1, 2 or 3 alkene groups.
  • Y 1 has an alkene group at the omega-3 position. In another embodiment, Y 1 has an alkene group at the omega-6 position. In another embodiment, Y 1 has an alkene group at the omega-9 position. In one embodiment, Y 1 has an alkene group at two or three of the omega-3, omega-6 and omega-9 positions. In one embodiment, Y 1 is unsaturated at the omega-6 and omega-9 positions. In another embodiment, Y 1 is unsaturated at the omega-3, omega-6 and omega-9 positions. In one embodiment, Y 1 is unsaturated at the omega-9 position.
  • Y 1 has at least one cis unsaturated alkene group. In one embodiment, Y 1 has at least two cis unsaturated alkene groups. In one embodiment, Y 1 has at least three cis unsaturated alkene groups. The at least one cis unsaturated alkene group may be at one, two or three of the omega-3, omega-6 and omega-9 positions. Unsaturation in lipid chains is discussed in MacLachlan et al., Journal of Controlled Release 107 (2005) 276-287.
  • Y 1 is selected from Y 1-i to Y 1-vii as provided in Table 2.
  • Y 2 is linked to L via an oxygen atom on the optionally substituted steroid. In one embodiment, Y 2 is linked to L via an oxygen atom on the 3-position of the A steroid ring. In one embodiment Y 2 is a sterol in which the hydrogen atom of the hydroxy group at the 3-position of the A steroid ring has been removed (and the connection to L is through the oxygen atom of said hydroxy group).
  • annasterol avenasterol; beta-sitosterol; brassicasterol; calciferol; campesterol; chalinosterol; chinasterol; cholestanol; cholesterol; coprostanol; cycloartol; dehydrocholesterol; desmosterol; dihydrocalciferol; dihydrocholesterol; dihydroergosterol; dinosterol; epicholesterol; ergosterol; fucosterol; hexahydrolumisterol; hexaol; hydroxycholesterol; lanosterol; lumisterol; parkeol; poriferasterol; saringosterol; sitostanol; sitosterol; stigmastanol; stigmasterol; weinbersterol: zymosterol; a sterol bile acid (such as cholic acid; chenodeoxycholic acid; glycocholic acid; taurocholic acid; deoxycholic acid, and lithocholic acid
  • the sterol is cholesterol
  • novel cationic lipids and stealth lipids of the invention may be used for the delivery of therapeutically acceptable agents including, e.g., biologically active agents.
  • therapeutically acceptable agents including, e.g., biologically active agents.
  • Formulations containing cationic lipids, stealth lipids, and other types of lipids are described throughout this disclosure. Whereas the lipids disclosed herein are believed novel and useful, certain characteristics are preferred over others for therapeutic use, as detailed further in the exemplary and nonbinding disclosure provided below.
  • the liposome, lipid nanoparticle or other such lipid formulation further comprises a biological effective agent.
  • the liposome, lipid nanoparticle or other such lipid formulation is empty.
  • the separate lipid components for use in a formulation are provided in a kit.
  • the kit contains instructions for generation of the lipid formulation.
  • the kit may comprise a ready-made formulation or separate or partial components that require mixing prior to administration.
  • a kit may further provide additional components such as, but not limited to, controls, buffers, containers, and delivery components, or may be limited to those inventive lipids and components as described herein.
  • the kit contains at least a liposome or liposome components including but not limited to one or more of a cationic lipid, a stealth lipid, a helper lipid, and/or an optional neutral lipid.
  • the kit further comprises a biologically active agent.
  • the kit further comprises one or more control lipids, or control agents, a control liposome formulation, stains, buffers, instructions for use, and the like.
  • the liposome formulation is premixed.
  • One or more of the kit's chemical components may be provided in a dehydrated form or in a hydrated form. Any of the various methods known in the art for dehydration on lyophilization of the various compounds and compositions described herein may be used.
  • any one of the specific compounds exemplified below or a pharmaceutically acceptable derivative thereof is provided.
  • the compound is for delivery of a biologically active agent to the liver and the compound is selected from one or more of E0024, E0014, E0052, E0118, E0175, E0177 or E0083.
  • a composition for delivery of a biologically active agent to the liver comprises one or more of compounds selected from E0024, E0014, E0052, E0118 or E0083.
  • a composition for delivery of a biologically active agent to the liver comprises compound E0024.
  • a composition for delivery of a biologically active agent to the liver comprises compound E0014.
  • a composition for delivery of a biologically active agent to the liver comprises compound E0052.
  • a composition for delivery of a biologically active agent to the liver comprises compound E0118.
  • a composition for delivery of a biologically active agent to the liver comprises compound E0083.
  • the compound is for delivery of a biologically active agent to a tumor and the compound is selected from one or more of E0011, E0008, E0025, E0026, E0076, E0077, E0085 or E0088.
  • a composition for delivery of a biologically active agent to a tumor comprises one or more of compounds selected from E0011, E0008, E0025, E0026, E0076, E0077, E0085 or E0088.
  • a composition for delivery of a biologically active agent to a tumor comprises compound E0011.
  • a composition for delivery of a biologically active agent to a tumor comprises compound E0008.
  • a composition for delivery of a biologically active agent to a tumor comprises compound E0025. In one embodiment, a composition for delivery of a biologically active agent to a tumor comprises compound E0026. In one embodiment, a composition for delivery of a biologically active agent to a tumor comprises compound E0076. In one embodiment, a composition for delivery of a biologically active agent to a tumor comprises compound E0077. In one embodiment, a composition for delivery of a biologically active agent to a tumor comprises compound E0085. In one embodiment, a composition for delivery of a biologically active agent to a tumor comprises compound E0088.
  • Liposomes, lipid nanoparticles and other such lipid formulations containing one or more of the lipids described herein are useful for delivery of nucleic acid compositions to a cell or tissue, either in vitro or in vivo.
  • Therapeutically relevant nucleic acid compositions include RNAi agents that are specific to one or more genes associated with a disease or disorder, wherein targetting the endogenous sequence in the cell or tissue with the RNAi agent leasts to a therapeutic or prophylactic effect.
  • cationic lipids of the invention provide at least 70% target inhibition when provided in a formulation for delivery of an RNAi to the liver.
  • Cationic lipids that provide at least 70% KD when formulated for liver include, but are not limited to, E0007, E0008, E0011, E0014, E0015, E0016, E0017, E0018, E0019, E0022, E0024, E0025, E0026, E0032, E0034, E0040, E0042, E0043, E0045, E0048, E0049, E0051, E0052, E0053, E0054, E0055 and E0118.
  • cationic lipids of the invention provide at least 80% target inhibition when provided in a formulation for delivery of an RNAi to the liver.
  • Cationic lipids that provide at least 80% KD when formulated for liver include, but are not limited to, E0008, E0011, E0014, E0016, E0017, E0018, E0019, E0022, E0024, E0025, E0026, E0032, E0034, E0040, E0042, E0043, E0045, E0048, E0052, E0053, E0054, E0055 and E0118.
  • cationic lipids of the invention provide at least 90% target inhibition when provided in a formulation for delivery of an RNAi to the liver.
  • Cationic lipids that provide at least 90% KD when formulated for liver include, but are not limited to, E0011, E0014, E0017, E0018, E0024, E0025, E0026, E0040, E0043, E0045, E0052, E0053, E0054, E0055 and E0118.
  • cationic lipids of the invention provide at least 95% target inhibition when provided in a formulation for delivery of an RNAi to the liver.
  • Cationic lipids that provide at least 95% KD when formulated for liver include, but are not limited to, E0014, E0017, E0018, E0024, E0026, E0040, E0043, E0052, E0054, E0055 and E0118.
  • cationic lipids of the invention provide at least 98% target inhibition when provided in a formulation for delivery of an RNAi to the liver.
  • Cationic lipids that provide at least 98% KD when formulated for liver include, but are not limited to, E0014, E0017, E0018, E0024, E0052, E0054 and E0118.
  • cationic lipids of the invention provide at least 50% target inhibition when provided in a formulation for delivery of an RNAi to a tumor or tumor cells.
  • Cationic lipids that provide at least 50% KD when formulated for tumors or tumor cells include, but are not limited to, E0008, E0011, E0025, E0026, E0075, E0076, E0077, E0085, E0088, E0095, E0104, E0178 and E0179.
  • cationic lipids of the invention provide at least 60% target inhibition when provided in a formulation for delivery of an RNAi to a tumor or tumor cells.
  • Cationic lipids that provide at least 60% KD when formulated for tumors or tumor cells include, but are not limited to, E0008, E0011, E0025, E0026, E0075, E0076, E0077, E0085 and E0088.
  • cationic lipids of the invention provide at least 70% target inhibition when provided in a formulation for delivery of an RNAi to a tumor or tumor cells.
  • Cationic lipids that provide at least 70% KD when formulated for tumors or tumor cells include, but are not limited to, E0011, E0025, E0026, E0075, E0076, E0077 and E0088.
  • cationic lipids of the invention provide at least 80% target inhibition when provided in a formulation for delivery of an RNAi to the tumor to a tumor or tumor cells.
  • Cationic lipids that provide at least 80% KD when formulated for tumors or tumor cells include, but are not limited to, E0008, E0025 and E0076.
  • therapeutically effective amounts of target inhibition for delivery of biologically active agents result in target inhibition of at least 30% where the target is a HepG2-like tumor or a 786-0-like tumor.
  • cationic lipids of the invention provide at least 30% target inhibition when provided in a formulation for delivery of an RNAi to a HepG2-like tumor or a 786-0-like tumor, and include E0056, E0076, E0085, E0104, E0175, E0176 and E0177.
  • cationic lipids of the invention provide at least 30% target inhibition when provided in a formulation for delivery of an RNAi to a HepG2-like tumor or a 786-O-like tumor, and include E0085, E0175 and E0177.
  • a preferred cationic lipid is E0014. In one embodiment, a preferred cationic lipid is E0017. In one embodiment, a preferred cationic lipid is E0018. In one embodiment, a preferred cationic lipid is E0024. In one embodiment, a preferred cationic lipid is E0052. In one embodiment, a preferred cationic lipid is E0054. In one embodiment, a preferred cationic lipid is E0118.
  • a preferred formulation for delivery of a biologically active agent to liver contains a cationic lipid with a pKa of from about 5.1 to about 7.4. In one embodiment, a preferred formulation for delivery of a biologically active agent to liver contains a cationic lipid with a pKa of from about 5.3 to about 7.3. In one embodiment, a preferred formulation for delivery of a biologically active agent to liver contains a cationic lipid with a pKa of from about 5.9 to about 7.0. In one embodiment, a preferred formulation for delivery of a biologically active agent to liver contains a cationic lipid with a pKa of from about 6.2 to about 6.8. In one embodiment, a preferred formulation for delivery of a biologically active agent to liver contains a cationic lipid with a pKa of about 6.1 or higher.
  • a preferred cationic lipid is E0008. In one embodiment, a preferred cationic lipid is E0025. In one embodiment, a preferred cationic lipid is E0076. In one embodiment, a preferred cationic lipid is E0085. In one embodiment, a preferred cationic lipid is E0175. In one embodiment, a preferred cationic lipid is E0177.
  • a preferred formulation for delivery of a biologically active agent to a tumor in vivo contains a cationic lipid with a pKa of from about 5.0 to about 6.7. In one embodiment, a preferred formulation for delivery of a biologically active agent to a tumor in vivo contains a cationic lipid with a pKa of from about 5.2 to about 6.3. In one embodiment, a preferred formulation for delivery of a biologically active agent to a tumor in vivo contains a cationic lipid with a pKa of from about 5.4 to about 6.2.
  • a preferred formulation for delivery of a biologically active agent to a tumor in vivo contains a cationic lipid with a pKa of from about 5.8 to about 6.1. In one embodiment, a preferred formulation for delivery of a biologically active agent to a tumor or tumor cell contains a cationic lipid with a pKa of about 6.1 or lower.
  • the present invention provides a pharmaceutical composition comprising at least one cationic lipid compound of the invention.
  • the present invention provides a pharmaceutical composition comprising at least one stealth lipid compound of the invention.
  • at least one other lipid component is present.
  • Such compositions may also contain a biologically active agent, optionally in combination with one or more other lipid components.
  • the one or more components, compositions and/or agents are provided in a kit.
  • Compositions containing lipids of the invention in combination with one or more biologically active agents in one embodiment are provided as formulations for use, e.g., in the delivery of therapeutically effective amounts of one or more biologically active agents to a cell or tissue.
  • the cell or tissue is in a subject in need of treatment or prophylaxis.
  • the subject is a patient in need of therapeutically effective amounts of the biologically active agent.
  • subjects include both humans and non-human animals.
  • the other lipid component(s) may be one or more selected from the group consisting of cationic lipids, (optional) neutral lipids, helper lipids, stealth lipids and alkyl resorcinol based lipids.
  • the invention provides a composition comprising: (a) a cationic lipid, e.g., compounds of any one of Formulas I through X, and/or E0001-E0171 and E0175-E0180 of the invention; (b) an optional neutral lipid, e.g. DSPC; (c) a helper lipid, e.g.
  • lipid components are in a liposome formulation, e.g., a nanoparticle or the like.
  • the liposome formulation further comprises a biologically active agent.
  • the liposome formulation further comprises a therapeutically effectve amount of a biologically active agent.
  • the other lipid component(s) may, e.g., be one or more selected from the group of known cationic lipids consisting of N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N-(1-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), 1,2-Dioleoyl-3-Dimethylammonium-propane (DODAP), 1,2-Dioleoylcarbamyl-3-Dimethylammonium-propane (DOCDAP), 1,2-Diline
  • the cationic lipid is selected from a lipid of Formula I. In one embodiment, the cationic lipid is selected from a lipid of Formula II. In one embodiment, the cationic lipid is selected from a lipid of Formula III. In one embodiment, the cationic lipid is selected from a lipid of Formula IV. In one embodiment, the cationic lipid is selected from a lipid of Formula V. In one embodiment, the cationic lipid is selected from a lipid of Formula VI. In one embodiment, the cationic lipid is selected from a lipid of Formula VII. In one embodiment, the cationic lipid is selected from a lipid of Formula VIII. In one embodiment, the cationic lipid is selected from a lipid of Formula IX.
  • the cationic lipid is selected from a lipid of Formula X. In one embodiment, the cationic lipid is selected from the list of E0001 through E0171 (E0001-E0171) and E0175 through E0180 (E0175-E0180).
  • the other lipid component(s) may, e.g., be (a) neutral lipid(s).
  • the neutral lipid(s) may, in one embodiment, be one or more selected from any of a variety of neutral uncharged or zwitterionic lipids.
  • neutral phospholipids examples include: 5-heptadecylbenzene-1,3-diol (resorcinol), cholesterol hemisuccinate (CHEMS), dipalmitoylphosphatidylcholine (DPPC), distearoylphosphatidylcholine (DSPC), phosphocholine (DOPC), dimyristoylphosphatidylcholine (DMPC), phosphatidylcholine (PLPC), phosphatidylethanolamine (PE), egg phosphatidylcholine (EPC), dilauryloylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), 1-myristoyl-2-palmitoyl phosphatidylcholine (MPPC), 1-palmitoyl-2-myristoyl phosphatidylcholine (PMPC), 1,2-diarachidoyl-sn-glycero-3-phosphocholine (DBPC), 1-palmit
  • the other lipid component(s) may, e.g., be (a) anionic lipid(s), e.g. anionic lipids capable of producing a stable complex.
  • anionic lipids are phosphatidylglycerol, cardiolipin, diacylphosphatidylserine, diacylphosphatidic acid, N-dodecanoyl phosphatidyl ethanoloamine, N-succinyl phosphatidylethanolamine, N-glutaryl phosphatidylethanolamine and lysylphosphatidylglycerol.
  • Suitable neutral and anionic lipids also include those described in US 2009/0048197, paragraph [0119].
  • the total amount of lipid in the composition being administered is, in one embodiment, from about 5 to about 30 mg lipid per mg biologically active agent (e.g. siRNA), in another embodiment from about 5 to about 25 mg lipid per mg biologically active agent (e.g. siRNA), in another embodiment from about 7 to about 25 mg lipid per mg biologically active agent (e.g. siRNA) and in one embodiment from about 7 to about 15 mg lipid per mg biologically active agent (e.g. siRNA).
  • biologically active agent e.g. siRNA
  • lipid compositions such as liposomes and liponanoparticles
  • passive and active loading methods either are contemplated as being within the scope of the invention.
  • the exact method used may be chosen based one multiple factors that include, but are not limited to, e.g., the biologically active agent to be loaded, the storage method to be used once loaded, the size of the resulting particle, and the dosage regimen contemplated.
  • Methods include, e.g., mechanical mixing of the drug and lipids at the time the liposomes are formed or reconstituted, dissolving all components in an organic solvent and concentrating them into a dry film, forming a pH or ion gradient to draw the active agent into the interior of the liposome, creating a transmembrane potential, and ionophore mediated loading. See, e.g., at least Examples 68, 69 and 77 below, PCT Publication No. WO 95/08986, U.S. Pat. No. 5,837,282, U.S. Pat. No. 5,837,282, and U.S. Pat. No. 7,811,602.
  • the dose of biologically active agent administered will depend on a number of factors such as the identity of the biologically active agent and the target patient (e.g. species of animal).
  • the concentration of biologically active agent will be adjusted accordingly but, when siRNA is being administered to an animal, a concentration of from 0.1 mg/ml to 10 mg/ml is typical per dose.
  • the total amount of siRNA can be measured by several methods.
  • HPLC methods include anion exchange, reverse phase (RP) or size exclusion (SEC). Fluorescent methods may also be used. In all of these methods the nanoparticles must be lysed to release the siRNA from the nanoparticle prior to measuring the total siRNA content.
  • the composition comprises a cationic lipid component which forms from about 10% to about 80%, from about 20% to about 70% or from about 30% to about 60% of the total lipid present in the composition. These percentages are mole percentages relative to the total moles of lipid components in the final lipid particle.
  • the composition comprises a neutral lipid component which forms from about 0% to about 50%, from about 0% to about 30% or from about 10% to about 20% of the total lipid present in the composition.
  • the neutral lipid component of the composition is optional.
  • the composition has no neutral lipid component.
  • the composition comprises a helper lipid component which forms from about 5% to about 80%, from about 20% to about 70% or from about 30% to about 50% of the total lipid present in the composition. These percentages are mole percentages relative to the total moles of lipid components in the final lipid particle.
  • the composition comprises a stealth lipid component which forms from about 0% to about 10%, from about 1% to about 6%, or from about 2% to about 5% of the total lipid present in the composition. These percentages are mole percentages relative to the total moles of lipid components in the final lipid particle.
  • the composition comprises a cationic lipid component forming from about 30 to about 60% of the total lipid present in the formulation, a neutral lipid comprising forming from about 0 to about 30% of the total lipid present in the formulation, a helper lipid forming from about 18 to about 46% of the total lipid present in the formulation and a stealth lipid forming from about 2 to about 4% of the total lipid present in the formulation.
  • a cationic lipid component forming from about 30 to about 60% of the total lipid present in the formulation
  • a neutral lipid comprising forming from about 0 to about 30% of the total lipid present in the formulation
  • a helper lipid forming from about 18 to about 46% of the total lipid present in the formulation
  • a stealth lipid forming from about 2 to about 4% of the total lipid present in the formulation.
  • Liposomal compositions of the invention are administered in any of a number of ways, including parenteral, intravenous, systemic, local, oral, intratumoral, intramuscular, subcutaneous, intraperitoneal, inhalation, or any such method of delivery.
  • the compositions are administered parenterally, i.e., intraarticularly, intravenously, intraperitoneally, subcutaneously, or intramuscularly.
  • the liposomal compositions are administered by intravenous infusion or intraperitoneally by a bolus injection.
  • compositions of the invention may be formulated as pharmaceutical compositions suitable for delivery to a subject.
  • the pharmaceutical compositions of the invention will often further comprise one or more buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose, dextrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives.
  • compositions of the present invention may be formulated as a lyophilizate.
  • compositions for use in the present invention can be found, e.g., in Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, Pa., 17.sup.th Ed. (1985).
  • intravenous compositions will comprise a solution of the liposomes suspended in an acceptable carrier, such as an aqueous carrier.
  • the cationic and stealth lipids of the invention are useful for formulations used for delivery of biologically active agents.
  • Formulations containing the novel lipids of the invention may be in various forms, including but not limited to particle forming delivery agents including microparticles, nanoparticles and trasfection agents that are useful for delivering various molecules to cells.
  • Specific formulations are effective at transfecting or delivering biologically active agents, such as antibodies (e.g., monoclonal, chimeric, humanized, nanobodies, and fragments thereof etc.), cholesterol, hormones, peptides, proteins, chemotherapeutics and other types of antineoplastic agents, low molecular weight drugs, vitamins, co-factors, nucleosides, nucleotides, oligonucleotides, enzymatic nucleic acids, antisense nucleic acids, triplex forming oligonucleotides, antisense DNA or RNA compositions, chimeric DNA:RNA compositions, allozymes, aptamers, ribozyme, decoys and analogs thereof, plasmids and other types of expression vectors, and small nucleic acid molecules, RNAi agents, short interfering nucleic acid (siNA), short interfering RNA (sRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA
  • Such formulations containing biologically active agents are useful, e.g., in providing compositions to prevent, inhibit, or treat diseases, conditions, or traits in a cell, subject or organism.
  • Diseases, conditions or traits include, but are not limited to, proliferative diseases, including cancer, inflammatory disease, transplant and/or tissue rejection, autoimmune diseases or conditions, age-related disease, neurological or neurodegenerative disease, respiratory disease, cardiovacular disease, ocular disease, metabolic disease, dermatological disease, auditory disease, a liver disease, a kidney or renal disease, etc.
  • the amount of active agent administered per dose is an amount above the minimal therapeutic dose but below a toxic dose.
  • the actual amount per dose may be determined by a physician depending on a number of factors, such as the medical history of the patient, the use of other therapies, the biologically active agent to be provided, and the nature of the disease.
  • the amount of biologically active agent administered may be adjusted throughout treatment, depending on the patient's response to treatment and the presence or severity of any treatment-associated side effects. Exemplary dosages and treatment for compounds that have been approved by an appropriate regulatory agency are known and available to those skilled in the art. See, e.g., Physician's Desk Reference, 64th ed., Physician's Desk Reference Inc. (2010), Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, Pa. (1985), and Remington The Science and Practice of Pharmacy, 21st ed., Lippincott Williams & Williams Publishers (2005).
  • a single dose is administered of a biologically active agent to a patient in need thereof.
  • multiple doses are administered, wherein the multiple doses may be administered concurrently, sequentially or alternating.
  • the same formulation is administered over multiple doses.
  • the formulations differ over multiple doses.
  • the doses may be administered once a day, or for one, two, three, four or more consecutive days.
  • the doses are administered once a week.
  • the doses are administered once every other week.
  • patients receive at least two courses of a treatment regimen, and potentially more, depending on the response of the patient to the treatment.
  • the invention provides a method for delivering a biologically active agent to a cell comprising administering a composition, which comprises the biologically active agent and a compound of the present invention, to the cell.
  • the cell may be in vitro or in vivo.
  • the invention provides a compound of formula (I) for use in therapy. It also provides subsets of compounds of formula I that are further distinguished in formulas II to X. Compounds of formulas I through X are generally referred to herein as cationic lipids.
  • the invention further provides a compound of formula (XI) for use in therapy. It also provides a subset of compound of formula XI that are further distinguished in formula XII. Compounds of formulas XI and XII are generally referred to herein as stealth lipids.
  • the invention further provides a method for the treatment of a disease or condition, comprising the step of administering a therapeutically effective amount of a composition containing at least one compound of formula (I) to a patient in combination with a biologically active agent that treats the disease or condition.
  • the invention also provides a composition containing at least one compound of formula (XI) for use in treating a disease or condition.
  • the invention also provides the use of a compound of formula (I) in the manufacture of a medicament for the treatment of a disease or condition.
  • the medicament contains a biologically active agent that treats the disease or condition.
  • the invention also provides the use of a biologically active agent which treats a disease or condition in the manufacture of a medicament for the treatment of the disease or condition, wherein the medicament also contains a compound of formula (I) or formula XI.
  • the invention also provides a method for the treatment of a disease or condition comprising the step of administering a therapeutically effective amount of a biologically active agent in a formulation containing at least one composition of the invention to a patient.
  • the disease or condition is a disease of the liver, a tumor or a disease.
  • the disease or condition is treatable by administering an siRNA agent.
  • the invention also provides a composition of the invention for use in treating a disease or condition in a patient.
  • the disease or condition is a disease of the liver, a tumor or a disease mediated by a protein encoded by a mRNA.
  • the invention also provides a product containing a compound of formula (I) and/or formula XI.
  • the product further comprises a biologically active agent as a combined preparation for simultaneous, separate or sequential use in therapy.
  • the compounds and compositions of the invention may be administered as at least one portion of a medicament by enteral or parenteral routes, including intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), oral, intranasal, rectal, vaginal, buccal, nasopharangeal, gastrointestinal or sublingual administration.
  • enteral or parenteral routes including intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), oral, intranasal, rectal, vaginal, buccal, nasopharangeal, gastrointestinal or sublingual administration.
  • the administration may be systemic or topical.
  • Topical administration may involve, e.g., catheterization, implantation, osmotic pumping, direct injection, dermal/transdermal application, stenting, ear/eye drops or portal vein administration.
  • the compounds of formula (I) and/or formula XI should be assessed for their biopharmaceutical properties, such as solubility and solution stability (across pH), permeability, etc., in order to select the most appropriate dosage form and route of administration for treatment of the proposed indication.
  • excipient includes any ingredient other than the compound(s) of the invention, the other lipid component(s) and the biologically active agent.
  • An excipient may impart either a functional (e.g drug release rate controlling) and/or a non-functional (e.g. processing aid or diluent) characteristic to the formulations.
  • a functional e.g drug release rate controlling
  • a non-functional e.g. processing aid or diluent
  • Typical pharmaceutically acceptable excipients include:
  • the excipient may be an aqueous solution carrier which may optionally contain a buffer (e.g. a PBS buffer) and/or a sugar.
  • a buffer e.g. a PBS buffer
  • the compounds and compositions of the invention may be administered orally.
  • Oral administration may involve swallowing, so that the compound enters the gastrointestinal tract, and/or buccal, lingual, or sublingual administration by which the compound enters the blood stream directly from the mouth.
  • the compounds and compositions of the invention can be administered parenterally.
  • the compounds and compositions of the invention may be administered directly into the blood stream, into subcutaneous tissue, into muscle, or into an internal organ.
  • Suitable means for administration include intravenous, intraarterial, intrathecal, intraventricular, intraurethral, intrasternal, intracranial, intramuscular, intrasynovial and subcutaneous.
  • Suitable devices for administration include needle (including microneedle) injectors, needle-free injectors and infusion techniques.
  • Parenteral formulations are typically aqueous or oily solutions. Where the solution is aqueous, excipients such as sugars (including but restricted to glucose, mannitol, sorbitol, etc.) salts, carbohydrates and buffering agents (preferably to a pH of from 3 to 9), but, for some applications, they may be more suitably formulated as a sterile non-aqueous solution or as a dried form to be used in conjunction with a suitable vehicle such as sterile, pyrogen-free water (WFI).
  • excipients such as sugars (including but restricted to glucose, mannitol, sorbitol, etc.) salts, carbohydrates and buffering agents (preferably to a pH of from 3 to 9), but, for some applications, they may be more suitably formulated as a sterile non-aqueous solution or as a dried form to be used in conjunction with a suitable vehicle such as sterile, pyrogen-free water (WFI).
  • WFI sterile, pyrogen
  • Parenteral formulations may include implants derived from degradable polymers such as polyesters (i.e. polylactic acid, polylactide, polylactide-co-glycolide, polycapro-lactone, polyhydroxybutyrate), polyorthoesters and polyanhydrides. These formulations may be administered via surgical incision into the subcutaneous tissue, muscular tissue or directly into specific organs.
  • degradable polymers such as polyesters (i.e. polylactic acid, polylactide, polylactide-co-glycolide, polycapro-lactone, polyhydroxybutyrate), polyorthoesters and polyanhydrides.
  • parenteral formulations under sterile conditions e.g., by lyophilisation
  • lyophilisation may readily be accomplished using standard pharmaceutical techniques well known to the skilled person.
  • solubility of the compounds and compositions used in the preparation of parenteral solutions may be increased by the use of appropriate formulation techniques, such as the incorporation of co-solvents and/or solubility-enhancing agents such as surfactants, micelle structures and cyclodextrins.
  • the compounds and compositions of the invention can be administered intranasally or by inhalation, typically in the form of a dry powder (either alone, as a mixture, e.g., in a dry blend with lactose, or as a mixed component particle, e.g., mixed with phospholipids, such as phosphatidylcholine) from a dry powder inhaler, as an aerosol spray from a pressurised container, pump, spray, atomiser (preferably an atomiser using electrohydrodynamics to produce a fine mist), or nebuliser, with or without the use of a suitable propellant, such as 1,1,1,2-tetrafluoroethane or 1,1,1,2,3,3,3-heptafluoropropane, or as nasal drops.
  • the powder may comprise a bioadhesive agent, e.g., chitosan or cyclodextrin.
  • the pressurised container, pump, spray, atomizer, or nebuliser contains a solution or suspension of the compound(s) of the invention comprising, e.g., ethanol, aqueous ethanol, or a suitable alternative agent for dispersing, solubilising, or extending release of the compositions of the invention, a propellant(s) as solvent and an optional surfactant, such as sorbitan trioleate, oleic acid, or an oligolactic acid.
  • a solution or suspension of the compound(s) of the invention comprising, e.g., ethanol, aqueous ethanol, or a suitable alternative agent for dispersing, solubilising, or extending release of the compositions of the invention, a propellant(s) as solvent and an optional surfactant, such as sorbitan trioleate, oleic acid, or an oligolactic acid.
  • the compound or composition Prior to use in a dry powder or suspension formulation, the compound or composition is micronised to a size suitable for delivery by inhalation (typically less than 5 microns). This may be achieved by any appropriate comminuting method, such as spiral jet milling, fluid bed jet milling, supercritical fluid processing to form nanoparticles, high pressure homogenisation, or spray drying.
  • Capsules (made, e.g., from gelatin or hydroxypropylmethylcellulose), blisters and cartridges for use in an inhaler or insufflator may be formulated to contain a powder mix of the compound or composition of the invention, a suitable powder base such as lactose or starch and a performance modifier such as l-leucine, mannitol, or magnesium stearate.
  • the lactose may be anhydrous or in the form of the monohydrate, preferably the latter.
  • Other suitable excipients include dextran, glucose, maltose, sorbitol, xylitol, fructose, sucrose and trehalose.
  • Formulations for inhaled/intranasal administration may be formulated to be immediate and/or modified release using, e.g., PGLA.
  • Modified release formulations include delayed-, sustained-, pulsed-, controlled-, targeted and programmed release.
  • transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound of the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin.
  • the compounds, compositions, methods and uses of the invention can be used to deliver a biologically active agent to one or more of the following in a patient:
  • liver or liver cells e.g. hepatocytes
  • kidney or kidney cells a kidney or kidney cells
  • CNS or CNS cells Central Nervous System, e.g. brain and/or spinal cord
  • PNS Peripheral Nervous System
  • the skin or skin cells e.g. dermis cells and/or follicular cells
  • an eye or ocular cells e.g. macula, fovea, cornea, retina
  • ocular cells e.g. macula, fovea, cornea, retina
  • an ear or cells of the ear e.g. cells of the inner ear, middle ear and/or outer ear.
  • the compounds, compositions, methods and uses of the invention are for delivering a biologically active agent to liver cells (e.g. hepatocytes). In one embodiment, the invention the compounds, compositions, methods and uses of the invention are for delivering a biologically active agent to a tumor or to tumor cells (e.g. a primary tumor or metastatic cancer cells).
  • a compound or composition of the invention is contacted with the liver or liver cells of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection, portal vein injection, catheterization, stenting), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection, portal vein injection, catheterization, stenting
  • a compound or composition of the invention is contacted with the kidney or kidney cells of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection, catheterization, stenting), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection, catheterization, stenting
  • a compound or composition of the invention is contacted with the tumor or tumor cells of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection, catheterization, stenting), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection, catheterization, stenting
  • a compound or composition of the invention is contacted with the CNS or CNS cells (e.g. brain cells and/or spinal cord cells) of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection, catheterization, stenting, osmotic pump administration (e.g. intrathecal or ventricular)), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection, catheterization, stenting, osmotic pump administration (e.g. intrathecal or ventricular)
  • osmotic pump administration e.g. intrathecal or ventricular
  • a compound or composition of the invention is contacted with the PNS or PNS cells of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection
  • a compound or composition of the invention is contacted with the lung or lung cells of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. pulmonary administration directly to lung tissues and cells), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. pulmonary administration directly to lung tissues and cells
  • a compound or composition of the invention is contacted with the vasculature or vascular cells of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. clamping, catheterization, stenting), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. clamping, catheterization, stenting
  • a compound or composition of the invention is contacted with the skin or skin cells (e.g. dermis cells and/or follicular cells) of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct dermal application, iontophoresis), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct dermal application, iontophoresis
  • a compound or composition of the invention is contacted with the eye or ocular cells (e.g. macula, fovea, cornea, retina) of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection, intraocular injection, periocular injection, iontophoresis, use of eyedrops, implants), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection, intraocular injection, periocular injection, iontophoresis, use of eyedrops, implants
  • a compound or composition of the invention is contacted with the ear or cells of the ear (e.g. cells of the inner ear, middle ear and/or outer ear) of the patient as is generally known in the art, such as via parental administration (e.g. intravenous, intramuscular, subcutaneous administration) or local administration (e.g. direct injection), to facilitate delivery.
  • parental administration e.g. intravenous, intramuscular, subcutaneous administration
  • local administration e.g. direct injection
  • the diseases or conditions which may be treated by this invention include those related to modulation in a patient of a gene, gene expression, protein, protein activity, cellular pathway, and the like.
  • the disease or condition treated by this invention may be one or more selected from the group consisting of: a proliferative disease (e.g. a tumor); an inflammatory disease; transplant and/or tissue rejection (allograft rejection); an autoimmune disease; an infectious disease; an age-related disease; a neurologic or neurodegenerative disease (e.g. Huntington's disease); a metabolic disease; a cardiovascular disease; a respiratory disease; an ocular disease; a dermatological disease; an auditory disease (e.g. hearing loss, deafness); a liver disease (e.g.
  • the invention treats a proliferative disease, e.g. a tumor or tumor cell.
  • the invention treats a liver disease, e.g. hepatitis, HCV, HBV, diabetis, cirrhosis and certain hepatocellular carcinomas.
  • the skilled person would be able to select a biologically active agent which in combination with a compound of the present invention delivers a therapeutically effective amount of the agent.
  • the agent is a RNAi therapeutic
  • the desired therapeutic effect is modulating expression of a target gene implicated in the disease or condition of interest.
  • the reduction of gene expression and thus reduction in the level of the respective protein/RNA relieves, to some extent, the symptoms of the disease or condition.
  • the compounds, compositions, methods and uses may involve administration conditions suitable for reducing or inhibiting, or ameliorating a disease or disorder.
  • a therapeutically effective amount of an RNAi agent is administered to a patient in need thereof, wherein the level of target gene expression is reduced in the patient compared to an untreated patient.
  • the expression of a target gene implicated in the disease or condition of interest is reduced by about 10%, more preferably about 20%, more preferably about 30%, more preferably about 40%, more preferably about 50%, more preferably about 60%, more preferably about 70%, more preferably about 80%, more preferably about 90%, more preferably about 95%, more preferably about 98%, and most preferably about 100% relative to an untreated patient.
  • articles such as “a” and “an” refer to one or more than one (at least one) of the grammatical object of the article.
  • the terms “(lipid) compound of the invention”, “(lipid) compound of formula (I)”, “(lipid) compound”, “cationic lipid” etc. include pharmaceutically acceptable derivatives thereof and polymorphs, isomers and isotopically labelled variants thereof.
  • said terms include compounds of formula (II), (III), (IV), (V), (VI), (VII), (VIII), (IX) and (X) for cationic lipids; and formulas (XI) and (XII) for stealth lipids; and embodiments thereof disclosed herein.
  • pharmaceutically acceptable derivative includes any pharmaceutically acceptable salt, solvate or hydrate of a compound of formula (I).
  • the pharmaceutically acceptable derivatives are pharmaceutically acceptable salts, solvates or hydrates of a compound of formula (I).
  • pharmaceutically acceptable salt includes a salt prepared from pharmaceutically acceptable non-toxic acids or bases including inorganic or organic acids and bases.
  • pharmaceutically acceptable salts see Stahl and Wermuth, Handbook of Pharmaceutical Salts: Properties, Selection and Use (Wiley-VCH, Weinheim, Germany, 2002).
  • solvate includes molecular complexes comprising a compound of the invention and one or more pharmaceutically acceptable solvent molecules such as water or C 1-6 alcohols, e.g. ethanol.
  • solvent molecules such as water or C 1-6 alcohols, e.g. ethanol.
  • hydrate means a “solvate” where the solvent is water.
  • Compounds of the invention may exist in one or more geometrical, optical, enantiomeric, diastereomeric and tautomeric forms, including but not limited to cis- and trans-forms, E- and Z-forms, R-, S- and meso-forms, keto-, and enol-forms. All such isomeric forms are included within the invention.
  • the isomeric forms may be in isomerically pure or enriched form, as well as in mixtures of isomers (e.g. racemic or diastereomeric mixtures).
  • the invention provides at least, e.g.:
  • isomers can be separated from their mixtures by the application or adaptation of known methods (e.g. chromatographic techniques and recrystallisation techniques). Where appropriate isomers can be prepared by the application or adaptation of known methods (e.g. asymmetric synthesis).
  • the invention includes pharmaceutically acceptable isotopically-labelled compounds of formula (I) wherein one or more atoms are replaced by atoms having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number usually found in nature.
  • isotopes suitable for inclusion in the compounds of the invention include isotopes of hydrogen, such as 2 H and 3 H, carbon, such as 11 C, 13 C and 14 C, chlorine, such as 36 Cl, fluorine, such as 18 F, iodine, such as 123 I and 125 I, nitrogen, such as 13 N and 15 N, oxygen, such as 15 O, 17 O and 18 O, phosphorus, such as 32 P, and sulphur, such as 35 S.
  • Certain isotopically-labelled compounds of formula (I) e.g., those incorporating a radioactive isotope, are useful in drug and/or substrate tissue distribution studies.
  • the radioactive isotopes 3 H and 14 C are particularly useful for this purpose in view of their ease of incorporation and ready means of detection.
  • Isotopically-labelled compounds of formula (I) can generally be prepared by conventional techniques known to the skilled person or by processes analogous to those described herein using an appropriate isotopically-labelled reagent in place of the non-labelled reagent previously employed.
  • treatment includes ameliorative, curative and prophylactic treatment.
  • a “patient” means an animal, preferably a mammal, preferably a human, in need of treatment.
  • the “biologically active agent” is preferably a therapeutic compound, i.e. a compound that is useful for the treatment or prevention of a disease or a condition.
  • the biologically active agent includes but are not limited to, e.g., antibodies, cholesterol, hormones, antivirals, peptides, polypeptides, proteins, nucleoproteins, chemotherapeutics, low molecular weight drugs, vitamins, co-factors, nucleosides, nucleoside derivatives, nucleotides, oligonucleotides, enzymatic nucleic acids, antisense nucleic acids, triplex forming oligonucleotides, 2,5-A antisense chimeras, allozymes, aptamers, ribozyme, decoy RNA molecules and analogs thereof, and small nucleic acid molecules, such as an RNA inhibitor (RNAi) including, e.g., short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA).
  • RNAi RNA inhibitor
  • the biologically active agent is preferably a nucleoside or nucleoside derivative, e.g. a nucleic acid, an oligonucleotide, a polynucleotide (e.g. siNA, miRNA, RNAi, antisense, aptamer, ribozyme, decoy, ribozyme, 2-5A, triplex forming oligonucleotide), and preferably an siRNA, miRNA, siRNA inhibitor or an miRNA inhibitor.
  • a nucleoside or nucleoside derivative e.g. a nucleic acid, an oligonucleotide, a polynucleotide (e.g. siNA, miRNA, RNAi, antisense, aptamer, ribozyme, decoy, ribozyme, 2-5A, triplex forming oligonucleotide), and preferably an siRNA, miRNA, siRNA inhibitor or an miRNA inhibitor.
  • the biologically active agent is an siNA (short interfering nucleic acid) molecule.
  • the siNA is siDNA.
  • the siNA is siRNA.
  • the siNA is miRNA.
  • the biologically active agent is a small nucleic acid molecule, referred to below for convenience purposes only as a “siNA” molecule, down-regulates expression of a target gene, e.g. wherein the target gene comprises a target encoding sequence or wherein the target gene comprises a target non-coding sequence or regulatory elements involved in target gene expression.
  • siNA small nucleic acid molecule
  • the siNA can be single, double, or multiple stranded. In one embodiment, it is double stranded.
  • the siNA comprises unmodified nucleotides and/or non-nucleotides. In one embodiment, the siNA comprises at least one, or more than one, modified nucleotides and/or non-nucleotides. In one embodiment, the modified nucleotide comprises a modified base portion. In one embodiment, the modified nucleotide comprises a modified sugar portion. In one embodiment, the modified nucleotide comprises a modified backbone portion. In one embodiment, the siNA comprises one or more of a modified base portion, a modified sugar portion, and/or a modified backbone portion.
  • the siNA molecule comprises about 15 to about 40 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 23, 33, 34, 35, 36, 37, 38, 39, or 40) base pairs, in a sub-embodiment about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) base pairs, in a sub-embodiment about 15 to about 28 base pairs, in a sub-embodiment about 17 to about 25 base pairs, in a sub-embodiment about 18 to about 23 base pairs, in a further sub-embodiment about 19 to about 22 base pairs.
  • the siNA comprises about 17 base pairs.
  • the siNA comprises about 18 base pairs.
  • the siNA comprises about 19 base pairs.
  • the siNA comprises about 20 base pairs.
  • the siNA comprises about 21 base pairs.
  • each of the two strands of the siNA molecule independently comprises about 15 to about 40 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 23, 33, 34, 35, 36, 37, 38, 39, or 40) nucleotides, in a sub-embodiment about 15 to about 30 (e.g.
  • each strand is about 17 nucleotides long. In one embodiment each strand is about 18 nucleotides long. In one embodiment each strand is about 19 nucleotides long. In one embodiment each strand is about 20 nucleotides long. In one embodiment each strand is about 21 nucleotides.
  • the siNA molecule directs cleavage of a target RNA via the RISC complex, i.e., RNA interference (RNAi).
  • RNAi RNA interference
  • the siNA molecule comprises a first and a second strand, the first strand of the siNA comprising a nucleotide sequence having sufficient complementarity to the target RNA for the siNA molecule to direct cleavage of the target RNA via RNA interference, and the second strand of said siNA molecule comprising a nucleotide sequence that is complementary to the first strand.
  • the short interfering nucleic acid (siNA) molecule is a chemically synthesized double stranded molecule.
  • the siNA inhibits the expression of target genes or a target gene family, wherein the genes or gene family sequences share sequence homology.
  • homologous sequences can be identified as is known in the art, e.g., using sequence alignments.
  • siNA molecules can be designed to target such homologous sequences, e.g., using perfectly complementary sequences or by incorporating non-canonical base pairs, e.g., mismatches and/or wobble base pairs that can provide additional target sequences.
  • the double-stranded siNA molecule does not contain any ribonucleotides. In another embodiment, the double-stranded siNA molecule comprises one or more ribonucleotides.
  • the siNA molecule which down-regulates expression of a target gene comprises an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of the target gene or a portion thereof, and a sense region, wherein the sense region comprises a nucleotide sequence substantially similar to the nucleotide sequence of the target gene or a portion thereof.
  • the antisense region and the sense region independently comprise about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides.
  • the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the target gene or a portion thereof, and the sense region comprises a nucleotide sequence that is complementary to the antisense region.
  • the siNA molecule comprises one blunt end. In one embodiment, the siNA molecule comprises two blunt ends, i.e., a symmetric terminus without any overhanging unpaired nucleotides.
  • all nucleotides of each fragment of the siNA molecule are base-paired to complementary nucleotides on the other strand of the siNA molecule.
  • the siNA molecule comprises one or more of the following features: a mismatch, a bulge, a loop and a wobble base pair, each of which may modulate the activity of the siNA molecule to mediate RNA interference.
  • the sense region is connected to the antisense region via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker.
  • a linker molecule such as a polynucleotide linker or a non-nucleotide linker.
  • the siNA molecule has one or more modified pyrimidine and/or purine nucleotides.
  • the pyrimidine nucleotides in the sense region are 2′-O-methylpyrimidine nucleotides or 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides.
  • the pyrimidine nucleotides in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides.
  • the pyrimidine nucleotides in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides.
  • the pyrimidine nucleotides in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the antisense region are 2′-O-methyl or 2′-deoxy purine nucleotides.
  • the sense strand has a non-complementary region.
  • the nucleotides present in said non-complementary region are all 2′-deoxy nucleotides.
  • the polynucleotide comprising the sense region includes a terminal cap moiety at the 5′-end, the 3′-end, or both of the 5′ and 3′ ends of the strand.
  • the polynucleotide comprising the antisense strand includes a terminal cap moiety at the 5′-end, the 3′-end, or both of the 5′ and 3′ ends of the strand.
  • the terminal cap moiety is an inverted deoxy abasic moiety or glyceryl moiety.
  • Other examples of terminal cap moieties are known in the art, e.g., WO 2005/021749 and WO 2007/128477.
  • the siNA has phosphite, phosphodiester, phosphorothioate and/or phosphorodithioate linkages in the polynucleotide backbone. In one embodiment, the siNA has at least one phosphorothioate linkage. In one embodiment, the siNA has at least one phosphorodithioate linkage.
  • the nucleotide modification(s) are present at specifically selected locations in the siNA that are sensitive to cleavage by ribonucleases, such as locations having pyrimidine nucleotides.
  • each of the two 3′ terminal nucleotides of each strand of the siNA molecule is a 2′-deoxy-pyrimidine nucleotide, such as a 2′-deoxy-thymidine.
  • the amount of the compound of the invention and the biologically active agent (e.g. the therapeutic compound) administered should be a therapeutically effective amount where used for the treatment of a disease or condition, and a prophylactically effective amount where used for the prevention of a disease or condition.
  • terapéuticaally effective amount refers to the amount of the compound of the invention and the biologically active agent (e.g. the therapeutic compound) needed to treat or ameliorate a targeted disease or condition.
  • prophylactically effective amount used herein refers to the amount of the compound of the invention and the biologically active agent (e.g. the therapeutic compound) needed to prevent a targeted disease or condition.
  • the exact dosage will generally be dependent on the patient's status at the time of administration. Factors that may be taken into consideration when determining dosage include the severity of the disease state in the patient, the general health of the patient, the age, weight, gender, diet, time, frequency and route of administration, identity of the biologically active agent (e.g.
  • an effective dose will be from 0.01 mg/kg/day (mass of drug compared to mass of patient) to 1000 mg/kg/day, e.g. 1 mg/kg/day to 100 mg/kg/day.
  • Compositions may be administered individually to a patient or may be administered in combination with other agents, drugs or hormones.
  • the compound or composition of the invention can be administered to the patient as a course of treatment, e.g., administration at various time intervals, such as once per day over the course of treatment, once every two days over the course of treatment, once every three days over the course of treatment, once every four days over the course of treatment, once every five days over the course of treatment, once every six days over the course of treatment, once per week over the course of treatment, once every other week over the course of treatment, once per month over the course of treatment, etc.
  • the course of treatment is once every 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
  • the course of treatment is from about one to about 52 weeks or longer (e.g. indefinitely). In one embodiment, the course of treatment is from about one to about 48 months or longer (e.g. indefinitely).
  • a course of treatment involves an initial course of treatment, such as once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more weeks for a fixed interval (e.g. 1 ⁇ , 2 ⁇ , 3 ⁇ , 4 ⁇ , 5 ⁇ , 6 ⁇ , 7 ⁇ , 8 ⁇ , 9 ⁇ , 10 ⁇ or more) followed by a maintenance course of treatment, such as once every 4, 6, 8, 10, 15, 20, 25, 30, 35, 40, or more weeks for an additional fixed interval (e.g. 1 ⁇ , 2 ⁇ , 3 ⁇ , 4 ⁇ , 5 ⁇ , 6 ⁇ , 7 ⁇ , 8 ⁇ , 9 ⁇ , 10 ⁇ or more).
  • a fixed interval e.g. 1 ⁇ , 2 ⁇ , 3 ⁇ , 4 ⁇ , 5 ⁇ , 6 ⁇ , 7 ⁇ , 8 ⁇ , 9 ⁇ , 10 ⁇ or more
  • proliferative disease as used herein is meant any disease, condition, trait, genotype or phenotype characterized by unregulated cell growth or replication as is known in the art.
  • the proliferative disease is cancer.
  • the proliferative disease is a tumor.
  • the proliferative disease includes, but are not limited to, e.g., liquid tumors such as, e.g., leukemias, e.g., acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute lymphocytic leukemia (ALL), multiple myeloma, and chronic lymphocytic leukemia; and solid tumors, e.g., AIDS related cancers such as Kaposi's sarcoma; breast cancers; bone cancers; brain cancers; cancers of the head and neck, non-Hodgkins lymphoma, adenoma, squamous cell carcinoma, laryngeal carcinoma, gallbladder and bile duct cancers, cancers of the retina, cancers of the esophagus, gastrointestinal cancers, ovarian cancer, uterine cancer, thyroid cancer, testicular cancer, endometrial cancer, melanoma, colorectal cancer,
  • the proliferative disease includes neovascularization associated with tumor angiogenesis, macular degeneration (e.g. wet/dry age related macular degeneration), corneal neovascularization, diabetic retinopathy, neovascular glaucoma, myopic degeneration.
  • the proliferative disease includes restenosis and polycystic kidney disease.
  • inflammatory disease as used herein is meant any disease, condition, trait, genotype or phenotype characterized by an inflammatory or allergic process as is known in the art.
  • Inflammatory diseases include, but are not limited to, e.g., inflammation (e.g. acute and/or chronic inflammation), respiratory disease, atherosclerosis, psoriasis, dermatitis, restenosis, asthma, allergic rhinitis, atopic dermatitis, septic shock, rheumatoid arthritis, inflammatory bowl disease, inflammatory pelvic disease, pain, ocular inflammatory disease, celiac disease, tuberculosis, silicosis and other pneumoconioses.
  • inflammation e.g. acute and/or chronic inflammation
  • respiratory disease e.g. acute and/or chronic inflammation
  • atherosclerosis e.g. acute and/or chronic inflammation
  • psoriasis e.g. acute and/or chronic inflammation
  • dermatitis e.g.
  • autoimmune disease as used herein is meant any disease, condition, trait, genotype or phenotype characterized by autoimmunity as is known in the art.
  • Autoimmune diseases include, but are not limited to, e.g., multiple sclerosis, diabetes mellitus, lupus, scleroderms, fibromyalgia, transplantation rejection (e.g. prevention of allograft rejection), pernicious anemia, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, myasthenia gravis, lupus erythematosus, multiple sclerosis, and Grave's disease.
  • infectious disease any disease, disorder or condition associated with an infectious agent, such as a virus, bacteria, fungus, prion or parasite.
  • Neurologic disease is meant any disease, disorder, or condition affecting the central or peripheral nervous system.
  • Neurologic diseases include, but are not limited to, diseases or disorders of either the peripheral or the central nervous system including, e.g., Alzheimer's Disease, Aneurysm, Brain Injury, Carpal Tunnel Syndrome, Cerebral Aneurysm, Chronic Pain, Creutzfeldt-Jakob Disease, Epilepsy, Huntington's Disease, Meningitis, Seizure Disorders, and other neurologic diseases, disorders and syndromes.
  • Respiratory disease is meant any disease or condition affecting the respiratory tract. Respiratory diseases include, but are not limited to, e.g., asthma, chronic obstructive pulmonary disease (COPD), allergic rhinitis, sinusitis, allergies, impeded respiration, respiratory distress syndrome, cystic fibrosis, pulmonary hypertension or vasoconstriction and emphysema.
  • COPD chronic obstructive pulmonary disease
  • Cardiovascular disease is meant and disease or condition affecting the heart and vasculature. Cardiovascular diseases include, but are not limited to, e.g., coronary heart disease (CHD), cerebrovascular disease (CVD), aortic stenosis, peripheral vascular disease, myocardial infarction (heart attack), arrhythmia, and congestive heart failure.
  • CHD coronary heart disease
  • CVD cerebrovascular disease
  • aortic stenosis aortic stenosis
  • peripheral vascular disease e.g., myocardial infarction (heart attack), arrhythmia, and congestive heart failure.
  • Ocular disease as used herein is meant any disease, condition, trait, genotype or phenotype of the eye and related structures.
  • Ocular diseases include, but are not limited to, e.g., cystoid macular edema, diabetic retinopathy, lattice degeneration, retinal vein occlusion, retinal artery occlusion, macular degeneration (e.g. age related macular degeneration such as wet AMD or dry AMD), toxoplasmosis, retinitis pigmentosa, conjunctival laceration, corneal laceration, glaucoma, and the like.
  • cystoid macular edema e.g., diabetic retinopathy, lattice degeneration, retinal vein occlusion, retinal artery occlusion, macular degeneration (e.g. age related macular degeneration such as wet AMD or dry AMD), toxoplasmosis, retinitis pigmentosa, conjunctival
  • metabolic disease is meant any disease or condition affecting metabolic pathways. Metabolic disease can result in an abnormal metabolic process, either congenital due to inherited enzyme abnormality (inborn errors of metabolism) or acquired due to disease of an endocrine organ or failure of a metabolically important organ such as the liver. In one embodiment, metabolic disease includes obesity, insulin resistance, and diabetes (e.g. type I and/or type II diabetes).
  • Dermatological disease is meant any disease or condition of the skin, dermis, or any substructure therein such as a hair, a follicle, etc. Dermatological diseases, disorders, conditions, and traits can include psoriasis, ectopic dermatitis, skin cancers such as melanoma and basal cell carcinoma, hair loss, hair removal and alterations in pigmentation.
  • auditory disease is meant any disease or condition of the auditory system, including the ear, such as the inner ear, middle ear, outer ear, auditory nerve, and any substructures therein. Auditory diseases, disorders, conditions, and traits can include hearing loss, deafness, tinnitus, vertigo, balance and motion disorders.
  • the disease or condition is a disease of the liver, a tumor, a disease mediated by FVII, and/or a disease mediated by PLK1.
  • Diseases mediated by FVII include abnormal blood coagulation and tumors; such diseases thus include thrombosis (e.g. venous thromboembolisms, pulmonary embolisms and strokes).
  • lipid refers to a group of organic compounds that includes, but is not limited to, esters of fatty acids and are characterised by being insoluble in water, but soluble in many organic solvents. Lipids can be divided into at least three classes (1) “simple lipids” which include fats and oils as well as waxes; (2) “compound lipids” which include phospholipids and glycolipids, and (3) “derived lipids” such as steroids.
  • cationic lipid as used herein is meant any lipophilic compound having a cationic charge, such as a compound having formula (I)
  • compositions wherein the definitions are as set out elsewhere herein.
  • Other examples of cationic lipids are set out above under the heading “compositions”.
  • helper lipid as used herein is meant a lipid that enhances transfection (e.g. transfection of the nanoparticle including the biologically active agent) to some extent.
  • the mechanism by which the helper lipid enhances transfection may include, e.g., enhancing particle stability and/or enhancing membrane fusogenicity.
  • Helper lipids include steroids and alkyl resorcinols. Examples of helper lipids are cholesterol, 5-heptadecylresorcinol, and cholesterol hemisuccinate
  • stealth lipid as used herein is meant a lipid that increases the length of time for which the nanoparticles can exist in vivo (e.g. in the blood).
  • a stealth lipid comprises a hydrophilic polymer head group operably linked to a lipid moiety.
  • stealth lipids in a liposome formulation shield the nanoparticle surface and thereby reduce opsonisation by blood proteins and uptake by the macrophages of the mononuclear phagocyte system.
  • Structures of stealth lipids suitable for use in the present invention include but are not limited to, e.g., compounds as provided in formula XI and formula XII.
  • the stealth lipid comprises a group selected from PEG (sometimes referred to as poly(ethylene oxide) and polymers based on poly(oxazoline), poly(vinyl alcohol), poly(glycerol), poly(N-vinylpyrrolidone), polyaminoacids and poly[N-(2-hydroxypropyl)methacrylamide].
  • PEG sometimes referred to as poly(ethylene oxide) and polymers based on poly(oxazoline), poly(vinyl alcohol), poly(glycerol), poly(N-vinylpyrrolidone), polyaminoacids and poly[N-(2-hydroxypropyl)methacrylamide].
  • the helper lipid is able to “shed” as described in Romberg et al.
  • Specific stealth lipids of the invention are provided, e.g., in formula XI and formula XII, which may be further substituted by one skilled in the art. Additional suitable PEG lipids are disclosed, e.g., in WO
  • Specific suitable stealth lipids include polyethyleneglycol-diacylglycerol or polyethyleneglycol-diacylglycamide (PEG-DAG) conjugates including those comprising a dialkylglycerol or dialkylglycamide group having alkyl chain length independently comprising from about C 4 to about C 40 saturated or unsaturated carbon atoms.
  • the dialkylglycerol or dialkylglycamide group can further comprise one or more substituted alkyl groups.
  • the PEG conjugate can be selected from PEG-dilaurylglycerol, PEG-dimyristylglycerol (catalog #GM-020 from NOF), PEG-dipalmitoylglycerol, PEG-disterylglycerol, PEG-dilaurylglycamide, PEG-dimyristylglycamide, PEG-dipalmitoylglycamide, and PEG-disterylglycamide, PEG-cholesterol (1-[8′-(Cholest-5-en-3[beta]-oxy)carboxamido-3′,6′-dioxaoctanyl]carbamoyl-[omega]-methyl-poly(ethylene glycol), PEG-DMB (3,4-Ditetradecoxylbenzyl-[omega]-methyl-poly(ethylene glycol) ether), S001, S002, S
  • PEG polyethylene glycol or other polyalkylene ether polymer.
  • PEG is an optionally substituted linear or branched polymer of ethylene glycol or ethylene oxide.
  • PEG is unsubstituted.
  • the PEG is substituted, e.g., by one or more alkyl, alkoxy, acyl or aryl groups.
  • the term includes PEG copolymers such as PEG-polyurethane or PEG-polypropylene (see, e.g., J.
  • the term does not include PEG copolymers.
  • the PEG has a molecular weight of from about 130 to about 50,000, in a sub-embodiment about 150 to about 30,000, in a sub-embodiment about 150 to about 20,000, in a sub-embodiment about 150 to about 15,000, in a sub-embodiment about 150 to about 10,000, in a sub-embodiment about 150 to about 6000, in a sub-embodiment about 150 to about 5000, in a sub-embodiment about 150 to about 4000, in a sub-embodiment about 150 to about 3000, in a sub-embodiment about 300 to about 3000, in a sub-embodiment about 1000 to about 3000, and in a sub-embodiment about 1500 to about 2500.
  • the PEG is a “PEG-2K”, also termed “PEG 2000”, which has an average molecular weight of about 2000 daltons.
  • PEG-2K is represented herein by the following formula (Xlla), wherein n is 45, meaning that the number-averaged degree of polymerization comprises about 45 subunits.
  • Xlla formula (Xlla)
  • lipid nanoparticle is meant a particle that comprises a plurality of (i.e. more than one) lipid molecules physically associated with each other by intermolecular forces.
  • the lipid nanoparticles may be, e.g., microspheres (including unilamellar and multlamellar vesicles, e.g. liposomes), a dispersed phase in an emulsion, micelles or an internal phase in a suspension.
  • the lipid nanoparticles have a size of about 1 to about 2,500 nm, about 1 to about 1,500 nm, about 1 to about 1,000 nm, in a sub-embodiment about 50 to about 600 nm, in a sub-embodiment about 50 to about 400 nm, in a sub-embodiment about 50 to about 250 nm, and in a sub-embodiment about 50 to about 150 nm.
  • all sizes referred to herein are the average sizes (diameters) of the fully formed nanoparticle, as measured by dynamic light scattering on a Malvern Zetasizer.
  • the nanoparticle sample is diluted in phosphate buffered saline (PBS) so that the count rate is approximately 200-400 kcts.
  • PBS phosphate buffered saline
  • the data is presented as a weighted average of the intensity measure.
  • the biologically active agent is associated with the lipid nanoparticle (e.g. vesicle), and is preferably encapsulated thereby.
  • the lipid nanoparticle comprises a biologically active agent, a compound of the invention, a neutral lipid, a helper lipid and a stealth lipid.
  • the liposome particles are stable in serum.
  • siNA short interfering nucleic acid
  • siRNA short interfering nucleic acid
  • siRNA short interfering RNA
  • miRNA microRNA
  • siRNAs short interfering oligonucleotides
  • chemically-modified short interfering nucleic acid molecules siRNAs are responsible for RNA interference, the process of sequence-specific post-transcriptional gene silencing in animals and plants.
  • siRNAs are generated by ribonuclease III cleavage from longer double-stranded RNA (dsRNA) which are homologous to, or specific to, the silenced gene target.
  • dsRNA double-stranded RNA
  • RNA interference is meant a biological process of inhibiting or down regulating gene expression in a cell as is generally known in the art, see e.g., Zamore and Haley, 2005, Science, 309, 1519-1524; Zamore et al., 2000, Cell, 101, 25-33; Elbashir et al., 2001, Nature, 411, 494-498; and Kreutzer et al., PCT Publication WO 00/44895; Fire, PCT Publication WO 99/32619; Mello and Fire, PCT Publication WO 01/29058; and the like.
  • RNAi is equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, transcriptional inhibition, or epigenetics.
  • the formulations containing lipids of the invention can be used in conjunction with siNA molecules to epigenetically silence genes at both the post-transcriptional level and/or the pre-transcriptional level.
  • modulation of gene expression by siNA molecules can result from siNA mediated cleavage of RNA (either coding or non-coding RNA) via RISC, or alternately, translational inhibition as is known in the art.
  • modulation of gene expression by siNA can result from transcriptional inhibition such as is reported e.g., in Janowski et al., 2005, Nature Chemical Biology, 1, 216-222.
  • RNAi inhibitor any molecule that can down modulate (e.g. reduce or inhibit) RNA interference function or activity in a cell or patient.
  • An RNAi inhibitor can down regulate, reduce or inhibit RNAi (e.g. RNAi mediated cleavage of a target polynucleotide, translational inhibition, or transcriptional silencing) by interaction with or interfering with the function of any component of the RNAi pathway, including protein components such as RISC, or nucleic acid components such as miRNAs or siRNAs.
  • RNAi inhibitor can be a siNA molecule, an antisense molecule, an aptamer, or a small molecule that interacts with or interferes with the function of RISC, a miRNA, or a siRNA or any other component of the RNAi pathway in a cell or patient.
  • RNAi e.g. RNAi mediated cleavage of a target polynucleotide, translational inhibition, or transcriptional silencing
  • an RNAi inhibitor can be used to modulate (e.g, up-regulate or down regulate) the expression of a target gene.
  • an RNA inhibitor is used to up-regulate gene expression by interfering with (e.g.
  • RNAi inhibitors of the invention can therefore be used to up-regulate gene expression for the treatment of diseases or conditions resulting from a loss of function.
  • RNAi inhibitor is used in interchangeably with the term “siNA” in various embodiments herein.
  • zymatic nucleic acid refers to a nucleic acid molecule that has complementarity in a substrate binding region to a specified gene target, and also has an enzymatic activity that acts to specifically cleave a target RNA, thereby inactivating the target RNA molecule.
  • the complementary regions allow sufficient hybridization of the enzymatic nucleic acid molecule to the target RNA and thus permit cleavage.
  • nucleic acids can be modified at the base, sugar, and/or phosphate groups.
  • enzymatic nucleic acid is used interchangeably with phrases such as ribozymes, catalytic RNA, enzymatic RNA, catalytic DNA, aptazyme or aptamer-binding ribozyme, regulatable ribozyme, catalytic oligonucleotides, nucleozyme, DNAzyme, RNA enzyme, endoribonuclease, endonuclease, minizyme, leadzyme, oligozyme or DNA enzyme. All of these terminologies describe nucleic acid molecules with enzymatic activity.
  • an enzymatic nucleic acid molecule has a specific substrate binding site that is complementary to one or more of the target nucleic acid regions, and that it has nucleotide sequences within or surrounding that substrate binding site that impart a nucleic acid cleaving and/or ligation activity to the molecule (see, e.g., Cech et al., U.S. Pat. No. 4,987,071; Cech et al., 1988, 260 JAMA 3030).
  • Ribozymes and enzymatic nucleic acid molecules of the invention can be chemically modified, e.g., as described in the art and elsewhere herein.
  • antisense nucleic acid refers to a non-enzymatic nucleic acid molecule that binds to target RNA by means of RNA-RNA or RNA-DNA or RNA-PNA (protein nucleic acid; Egholm et al., 1993 Nature 365, 566) interactions and alters the activity of the target RNA (for a review, see Stein and Cheng, 1993 Science 261, 1004 and Woolf et al., U.S. Pat. No. 5,849,902).
  • Antisense DNA can be synthesized chemically or expressed via the use of a single stranded DNA expression vector or equivalent thereof.
  • Antisense molecules of the invention can be chemically modified, e.g. as described in the art.
  • RNase H activating region refers to a region (generally greater than or equal to 4-25 nucleotides in length, preferably from 5-11 nucleotides in length) of a nucleic acid molecule capable of binding to a target RNA to form a non-covalent complex that is recognized by cellular RNase H enzyme (see e.g., Arrow et al., U.S. Pat. No. 5,849,902; Arrow et al., U.S. Pat. No. 5,989,912).
  • the RNase H enzyme binds to the nucleic acid molecule-target RNA complex and cleaves the target RNA sequence.
  • 2-5A antisense chimera refers to an antisense oligonucleotide containing a 5′-phosphorylated 2′-5′-linked adenylate residue. These chimeras bind to target RNA in a sequence-specific manner and activate a cellular 2-5A-dependent ribonuclease that, in turn, cleaves the target RNA (Torrence et al., 1993 Proc. Natl. Acad. Sci. USA 90, 1300; Silverman et al., 2000, Methods Enzymol., 313, 522-533; Player and Torrence, 1998, Pharmacol. Ther., 78, 55-113). 2-5A antisense chimera molecules can be chemically modified, e.g. as described in the art.
  • triple helix structure refers to an oligonucleotide that can bind to a double-stranded DNA in a sequence-specific manner to form a triple-strand helix. Formation of such triple helix structure has been shown to inhibit transcription of the targeted gene (Duval-Valentin et al., 1992 Proc. Natl. Acad. Sci. USA 89, 504; Fox, 2000, Curr. Med. Chem., 7, 17-37; Praseuth et. al., 2000, Biochim. Biophys. Acta, 1489, 181-206).
  • Triplex forming oligonucleotide molecules of the invention can be chemically modified, e.g. as described in the art.
  • decoy RNA refers to an RNA molecule or aptamer that is designed to preferentially bind to a predetermined ligand. Such binding can result in the inhibition or activation of a target molecule.
  • the decoy RNA or aptamer can compete with a naturally occurring binding target for the binding of a specific ligand.
  • a decoy RNA can be designed to bind to a receptor and block the binding of an effector molecule, or can be designed to bind to receptor of interest and prevent interaction with the receptor.
  • Decoy molecules of the invention can be chemically modified, e.g. as described in the art.
  • ssDNA single stranded DNA
  • ssDNA single stranded DNA
  • a ssDNA can be a sense or antisense gene sequence or EST (Expressed Sequence Tag).
  • allozyme refers to an allosteric enzymatic nucleic acid molecule, including e.g., U.S. Pat. Nos. 5,834,186, 5,741,679, 5,589,332, 5,871,914, and PCT publication Nos. WO 00/24931, WO 00/26226, WO 98/27104, and WO 99/29842.
  • aptamer as used herein is meant a polynucleotide composition that binds specifically to a target molecule, wherein the polynucleotide has a sequence that differs from a sequence normally recognized by the target molecule in a cell.
  • an aptamer can be a nucleic acid molecule that binds to a target molecule where the target molecule does not naturally bind to a nucleic acid.
  • the target molecule can be any molecule of interest.
  • Aptamer molecules of the invention can be chemically modified, e.g. as described in the art.
  • modulate is meant that the expression of the gene, or level of RNA molecule or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits is up regulated or down regulated, or is absent, such that expression, level, or activity is greater than or less than that observed without the modulator.
  • modulate means “inhibit”.
  • modulation of a pathway denotes, within the terms of the invention, an up-regulation or a down-regulation of a therapeutically meaningful component and/or endpoint of a biological pathway that contains, or is regulated by, e.g., the protein, enzyme, or substance being targetted or encoded by the target mRNA.
  • inhibitor By “inhibit”, “down-regulate”, or “reduce”, it is meant that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is reduced below that observed in a natural environment, e.g. in the absence of the nucleic acid molecules (e.g. siNA).
  • inhibition, down-regulation or reduction with a siNA molecule is below that level observed in the presence of an inactive or attenuated molecule.
  • inhibition, down-regulation, or reduction with siNA molecules is below that level observed in the presence of, e.g., a siNA molecule with scrambled sequence or with mismatches.
  • inhibition, down-regulation, or reduction of gene expression with a nucleic acid molecule is greater in the presence of the nucleic acid molecule than in its absence.
  • inhibition, down regulation, or reduction of gene expression is associated with post transcriptional silencing, such as RNAi mediated cleavage of a target nucleic acid molecule (e.g. RNA) or inhibition of translation.
  • inhibition, down regulation, or reduction of gene expression is associated with pretranscriptional silencing.
  • up-regulate or “promote”, it is meant that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is increased above that observed in a natural environment, e.g. in the absence of the nucleic acid molecules (e.g. siNA).
  • up-regulation or promotion of gene expression with an siNA molecule is above that level observed in the presence of an inactive or attenuated molecule.
  • up-regulation or promotion of gene expression with siNA molecules is above that level observed in the presence of, e.g., an siNA molecule with scrambled sequence or with mismatches.
  • up-regulation or promotion of gene expression with a nucleic acid molecule is greater in the presence of the nucleic acid molecule than in its absence.
  • up-regulation or promotion of gene expression is associated with inhibition of RNA mediated gene silencing, such as RNAi mediated cleavage or silencing of a coding or non-coding RNA target that down regulates, inhibits, or silences the expression of the gene of interest to be up-regulated.
  • RNA e.g., nucleic acid sequences including, but not limited to, structural genes encoding a polypeptide.
  • a gene or target gene can also encode a functional RNA (FRNA) or non-coding RNA (ncRNA), such as small temporal RNA (stRNA), micro RNA (miRNA), small nuclear RNA (snRNA), short interfering RNA (siRNA), small nucleolar RNA (snRNA), ribosomal RNA (rRNA), transfer RNA (tRNA) and precursor RNAs thereof.
  • FRNA functional RNA
  • ncRNA non-coding RNA
  • stRNA small temporal RNA
  • miRNA micro RNA
  • snRNA small nuclear RNA
  • siRNA small interfering RNA
  • snRNA small nucleolar RNA
  • rRNA ribosomal RNA
  • tRNA transfer RNA
  • Such non-coding RNAs can serve as target nucleic acid molecules for siNA mediated RNA interference in modulating the activity of FRNA or ncRNA involved in functional or regulatory cellular processes. Abberant FRNA or ncRNA activity leading to disease can therefore be modulated by siNA molecules.
  • target as used herein is meant any target protein, peptide, or polypeptide encoded by a target gene.
  • target also refers to nucleic acid sequences encoding any target protein, peptide, or polypeptide having target activity, such as encoded by target RNA.
  • target is also meant to include other target encoding sequence, such as other target isoforms, mutant target genes, splice variants of target genes, and target gene polymorphisms.
  • target nucleic acid is meant any nucleic acid sequence whose expression or activity is to be modulated.
  • the target nucleic acid can be DNA or RNA.
  • non-canonical base pair any non-Watson Crick base pair, such as mismatches and/or wobble base.
  • sense region is meant a nucleotide sequence of a siNA molecule having complementarity to an antisense region of the siNA molecule.
  • the sense region of a siNA molecule can comprise a nucleic acid sequence having homology with a target nucleic acid sequence.
  • the sense region of the siNA molecule is referred to as the sense strand or passenger strand.
  • antisense region is meant a nucleotide sequence of a siNA molecule having complementarity to a target nucleic acid sequence.
  • the antisense region of a siNA molecule can optionally comprise a nucleic acid sequence having complementarity to a sense region of the siNA molecule.
  • the antisense region of the siNA molecule is referred to as the antisense strand or guide strand.
  • target nucleic acid or “target polynucleotide” is meant any nucleic acid sequence whose expression or activity is to be modulated.
  • the target nucleic acid can be DNA or RNA.
  • a target nucleic acid of the invention is target RNA.
  • a target nucleic acid of the invention is target DNA.
  • a double stranded nucleic acid molecule of the invention such as an siNA molecule, wherein each strand is between 15 and 40 nucleotides in length, comprises between about 10% and about 100% (e.g. about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 100%) complementarity between the two strands of the double stranded nucleic acid molecule.
  • a percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule that can pair through the formation of hydrogen bonds (e.g. Watson-Crick base pairing) with a second nucleic acid sequence.
  • halogen refers to fluoro, chloro, bromo, and iodo.
  • halogen includes fluorine, chlorine, bromine and iodine.
  • haloalkyl refers to an alkyl as defined herein that is substituted by one or more halo groups as defined herein.
  • the haloalkyl can be monohaloalkyl, dihaloalkyl or polyhaloalkyl including perhaloalkyl.
  • a monohaloalkyl can have one iodo, bromo, chloro or fluoro within the alkyl group.
  • Dihaloalky and polyhaloalkyl groups can have two or more of the same halo atoms or a combination of different halo groups within the alkyl.
  • the polyhaloalkyl contains up to 12, or 10, or 8, or 6, or 4, or 3, or 2 halo groups.
  • Non-limiting examples of haloalkyl include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl.
  • a perhaloalkyl refers to an alkyl having all hydrogen atoms replaced with halo atoms.
  • alkyl alkylene
  • alkenyl alkynyl
  • alkynyl alkynyl
  • alkyl includes monovalent, straight or branched, saturated, acyclic hydrocarbyl groups. As used herein, the term “alkyl” refers to a fully saturated branched or unbranched hydrocarbon moiety having up to 50 carbon atoms. Unless otherwise provided, alkyl refers to hydrocarbon moieties having 1 to 50 carbon atoms, 1 to 40 carbon atoms, 1 to 30 carbon atoms, 1 to 20 carbon atoms, 1 to 16 carbon atoms, 1 to 16 carbon atoms, 1 to 10 carbon atoms, 1 to 7 carbon atoms, or 1 to 4 carbon atoms.
  • alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl, iso-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n-heptyl, n-octyl, n-nonyl, n-decyl and the like.
  • alkyl is C 1-10 alkyl, in another embodiment C 1-6 alkyl, in another embodiment C 1-4 alkyl, such as methyl, ethyl, n-propyl, i-propyl or t-butyl groups.
  • cycloalkyl includes monovalent, saturated, cyclic hydrocarbyl groups.
  • cycloalkyl is C 3-10 cycloalkyl, in another embodiment C 3-6 cycloalkyl such as cyclopentyl and cyclohexyl.
  • alkoxy means alkyl-O—, wherein alkyl is defined herein above.
  • Representative examples of alkoxy include, but are not limited to, methoxy, ethoxy, propoxy, 2-propoxy, butoxy, tert-butoxy, pentyloxy, hexyloxy, cyclopropyloxy-, cyclohexyloxy- and the like.
  • alkoxy groups typically have about 1-7, more preferably about 1-4 carbons.
  • alkenyl includes monovalent, straight or branched, unsaturated, acyclic hydrocarbyl groups having at least one carbon-carbon double bond and, in one embodiment, no carbon-carbon triple bonds.
  • alkylene refers to divalent alkyl group as defined herein above having 1 to 50 carbon atoms. It comprises 1 to 50 carbon atoms, Unless otherwise provided, alkylene refers to moieties having 1 to 50 carbon atoms, 1 to 40 carbon atoms, 1 to 30 carbon atoms, 1 to 20 carbon atoms, 1 to 16 carbon atoms, 1 to 10 carbon atoms, 1 to 7 carbon atoms, or 1 to 4 carbon atoms.
  • alkylene examples include, but are not limited to, methylene, ethylene, n-propylene, iso-propylene, n-butylene, sec-butylene, iso-butylene, tert-butylene, n-pentylene, isopentylene, neopentylene, n-hexylene, 3-methylhexylene, 2,2-dimethylpentylene, 2,3-dimethylpentylene, n-heptylene, n-octylene, n-nonylene, n-decylene and the like.
  • alkenyl is C 2-10 alkenyl, in another embodiment C 2-6 alkenyl, in another embodiment C 2-4 alkenyl.
  • cycloalkenyl includes monovalent, partially unsaturated, cyclic hydrocarbyl groups having at least one carbon-carbon double bond.
  • cycloalkenyl is C 3-10 cycloalkenyl, in another embodiment C 5-10 cycloalkenyl, e.g. cyclohexenyl.
  • alkynyl includes monovalent, straight or branched, unsaturated, acyclic hydrocarbyl groups having at least one carbon-carbon triple bond and, in one embodiment, no carbon-carbon double bonds.
  • alkynyl is C 2-10 alkynyl, in another embodiment C 2-6 alkynyl, in another embodiment C 2-4 alkynyl.
  • cycloalkynyl includes monovalent, partially unsaturated, cyclic hydrocarbyl groups having at least one carbon-carbon triple bond.
  • cycloalkynyl is C 6-10 cycloalkenyl, in another embodiment C 8-10 cycloalkynyl.
  • alkylene includes divalent, straight or branched, saturated, acyclic hydrocarbyl groups.
  • alkylene is C 1-10 alkylene, in another embodiment C 1-6 alkylene, in another embodiment C 1-4 alkylene, such as methylene, ethylene, n-propylene, i-propylene or t-butylene groups.
  • alkenylene includes divalent, straight or branched, unsaturated, acyclic hydrocarbyl groups having at least one carbon-carbon double bond and, in one embodiment, no carbon-carbon triple bonds.
  • alkenylene is C 2-10 alkenylene, in another embodiment C 2-6 alkenylene, in another embodiment C 2-4 alkenylene.
  • alkynylene includes divalent, straight or branched, unsaturated, acyclic hydrocarbyl groups having at least one carbon-carbon triple bond.
  • alkynylene is C 2-10 alkynylene, in another embodiment C 2-6 alkynylene, in another embodiment C 2-4 alkynylene.
  • hetero atoms refers to nitrogen (N), oxygen (O), phosphorus (P) or sulfur (S) atoms, in particular nitrogen or oxygen.
  • heteroalkyl includes alkyl groups in which up to six carbon atoms, in one embodiment up to five carbon atoms, in another embodiment up to four carbon atoms, in another embodiment up to three carbon atoms, in another embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q , N, P(O) r or Si (and preferably O, S(O) q or N), provided at least one of the alkyl carbon atoms remains.
  • the heteroalkyl group may be C-linked or hetero-linked, i.e. it may be linked to the remainder of the molecule through a carbon atom or through O, S(O) q , N, P(O) r or Si. Note that S(O) q and P(O) r are defined below.
  • heterocycloalkyl includes cycloalkyl groups in which up to six carbon atoms, in one embodiment up to five carbon atoms, in another embodiment up to four carbon atoms, in another embodiment up to three carbon atoms, in another embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one of the cycloalkyl carbon atoms remains.
  • heterocycloalkyl groups include oxiranyl, thiaranyl, aziridinyl, oxetanyl, thiatanyl, azetidinyl, tetrahydrofuranyl, tetrahydrothiophenyl, pyrrolidinyl, tetrahydropyranyl, tetrahydrothiopyranyl, piperidinyl, 1,4-dioxanyl, 1,4-oxathianyl, morpholinyl, 1,4-dithianyl, piperazinyl, 1,4-azathianyl, oxepanyl, thiepanyl, azepanyl, 1,4-dioxepanyl, 1,4-oxathiepanyl, 1,4-oxaazepanyl, 1,4-dithiepanyl, 1,4-thieazepanyl and 1,4-diazepanyl.
  • heteroalkenyl includes alkenyl groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one alkenyl carbon-carbon double bond remains.
  • the heteroalkenyl group may be C-linked or hetero-linked, i.e. it may be linked to the remainder of the molecule through a carbon atom or through O, S(O) q or N.
  • heterocycloalkenyl includes cycloalkenyl groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one cycloalkenyl carbon-carbon double bond remains.
  • heterocycloalkenyl groups include 3,4-dihydro-2H-pyranyl, 5-6-dihydro-2H-pyranyl, 2H-pyranyl, 1,2,3,4-tetrahydropyridinyl and 1,2,5,6-tetrahydropyridinyl.
  • the heterocycloalkenyl group may be C-linked or N-linked, i.e.
  • heterocycloalkenyl groups of the invention include C 3 -C 10 cycloalkenyl groups. In one embodiment, heterocycloalkenyl groups of the invention include C 5 -C 10 cycloalkenyl groups.
  • heteroalkynyl includes alkynyl groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one alkynyl carbon-carbon triple bond remains.
  • the heteroalkynyl group may be C-linked or hetero-linked, i.e. it may be linked to the remainder of the molecule through a carbon atom or through O, S(O) q or N.
  • heterocycloalkynyl includes cycloalkynyl groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one of the cycloalkynyl carbon-carbon triple bonds remains.
  • the heterocycloalkenyl group may be C-linked or N-linked, i.e. it may be linked to the remainder of the molecule through a carbon atom or through a nitrogen atom.
  • An example of a heterocycloalkynyl group includes azacyclooct-4-yne.
  • the invention includes C 3 -C 10 heterocycloalkynyl groups.
  • the invention includes C 5 -C 10 heterocycloalkynyl groups.
  • heteroalkylene includes alkylene groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one alkylene carbon-carbon bond remains.
  • heteroalkenylene includes alkenylene groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one alkenylene carbon-carbon double bond remains.
  • heteroalkynylene includes alkynylene groups in which up to three carbon atoms, in one embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q or N, provided at least one alkynylene carbon-carbon triple bond remains.
  • aryl includes monovalent, aromatic, cyclic hydrocarbyl groups, such as phenyl or naphthyl (e.g. 1-naphthyl or 2-naphthyl). In general, the aryl groups may be monocyclic or polycyclic fused ring aromatic groups. Preferred aryl are C 6 -C 14 aryl. As used herein the term “aryl” refers to an aromatic hydrocarbon group having 6-20 carbon atoms in the ring portion. Typically, aryl is monocyclic, bicyclic or tricyclic aryl having 6-20 carbon atoms and includes one or more aromatic rings fused to one or more non-aromatic hydrocarbon rings. Non-limiting examples include phenyl, naphthyl or tetrahydronaphthyl.
  • aryl groups are monovalent derivatives of aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, chrysene, coronene, fluoranthene, fluorene, as-indacene, s-indacene, indene, naphthalene, ovalene, perylene, phenalene, phenanthrene, picene, pleiadene, pyrene, pyranthrene and rubicene.
  • arylalkyl means alkyl substituted with an aryl group, e.g. benzyl.
  • arylene includes divalent aromatic, cyclic hydrocarbyl groups, such as phenylene.
  • the arylene groups may be monocyclic or polycyclic fused ring aromatic groups.
  • Preferred arylene are C 6 -C 14 arylene.
  • arylene groups are divalent derivatives of aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, chrysene, coronene, fluoranthene, fluorene, as-indacene, s-indacene, indene, naphthalene, ovalene, perylene, phenalene, phenanthrene, picene, pleiadene, pyrene, pyranthrene and rubicene.
  • heteroaryl includes monovalent, heteroaromatic, cyclic hydrocarbyl groups additionally containing one or more heteroatoms independently selected from O, S, N and NR N , where R N is defined below (and in one embodiment is H or alkyl (e.g., C 1-6 alkyl)).
  • R N is defined below (and in one embodiment is H or alkyl (e.g., C 1-6 alkyl)).
  • heteroaryl refers to a 5-14 membered monocyclic- or bicyclic- or tricyclic-aromatic ring system, having 1 to 8 heteroatoms selected from N, O or S.
  • the heteroaryl is a 5-10 membered ring system (e.g., 5-7 membered monocycle or an 8-10 membered bicycle) or a 5-7 membered ring system.
  • Typical heteroaryl groups include 2- or 3-thienyl, 2- or 3-furyl, 2- or 3-pyrrolyl, 2-, 4-, or 5-imidazolyl, 3-, 4-, or 5-pyrazolyl, 2-, 4-, or 5-thiazolyl, 3-, 4-, or 5-isothiazolyl, 2-, 4-, or 5-oxazolyl, 3-, 4-, or 5-isoxazolyl, 3- or 5-1,2,4-triazolyl, 4- or 5-1,2,3-triazolyl, tetrazolyl, 2-, 3-, or 4-pyridyl, 3- or 4-pyridazinyl, 3-, 4-, or 5-pyrazinyl, 2-pyrazinyl, and 2-, 4-, or 5-pyrimidinyl.
  • heteroaryl also refers to a group in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring.
  • Nonlimiting examples include those head groups provided herein as H 15 and H 29 .
  • the heteroaryl groups may be monocyclic or polycyclic (e.g., bicyclic) fused ring heteroaromatic groups.
  • heteroaryl groups contain 5-13 ring members (e.g., 5-10 members) and 1, 2, 3 or 4 ring heteroatoms independently selected from O, S, N and NR N .
  • a heteroaryl group may be 5, 6, 9 or 10 membered, e.g., 5-membered monocyclic, 6-membered monocyclic, 9-membered fused-ring bicyclic or 10-membered fused-ring bicyclic.
  • Monocyclic heteroaromatic groups include heteroaromatic groups containing 5-6 ring members and 1, 2, 3 or 4 heteroatoms selected from O, S, N or NR N .
  • 5-membered monocyclic heteroaryl groups contain 1 ring member which is a —NR N — group, an —O— atom or an —S— atom and, optionally, 1-3 ring members (e.g. 1 or 2 ring members) which are ⁇ N— atoms (where the remainder of the 5 ring members are carbon atoms).
  • Examples of 5-membered monocyclic heteroaryl groups are pyrrolyl, furanyl, thiophenyl, pyrazolyl, imidazolyl, isoxazolyl, oxazolyl, isothiazolyl, thiazolyl, 1,2,3 triazolyl, 1,2,4 triazolyl, 1,2,3 oxadiazolyl, 1,2,4 oxadiazolyl, 1,2,5 oxadiazolyl; 1,3,4 oxadiazolyl, 1,3,4 thiadiazolyl, pyridyl, pyrimidinyl, pyridazinyl, pyrazinyl, 1,3,5 triazinyl, 1,2,4 triazinyl, 1,2,3 triazinyl and tetrazolyl.
  • 6-membered monocyclic heteroaryl groups are pyridinyl, pyridazinyl, pyrimidinyl and pyrazinyl.
  • 6-membered monocyclic heteroaryl groups contain 1 or 2 ring members which are ⁇ N— atoms (where the remainder of the 6 ring members are carbon atoms).
  • Bicyclic heteroaromatic groups include fused-ring heteroaromatic groups containing 9-13 ring members and 1, 2, 3, 4 or more heteroatoms selected from O, S, N or NR N .
  • 9-membered bicyclic heteroaryl groups contain 1 ring member which is a —NR N — group, an —O— atom or an —S— atom and, optionally, 1-3 ring members (e.g. 1 or 2 ring members) which are ⁇ N— atoms (where the remainder of the 9 ring members are carbon atoms).
  • 9-membered fused-ring bicyclic heteroaryl groups are benzofuranyl, benzothiophenyl, indolyl, benzimidazolyl, indazolyl, benzotriazolyl, pyrrolo[2,3-b]pyridinyl, pyrrolo[2,3-c]pyridinyl, pyrrolo[3,2-c]pyridinyl, pyrrolo[3,2-b]pyridinyl, imidazo[4,5-b]pyridinyl, imidazo[4,5-c]pyridinyl, pyrazolo[4,3-d]pyridinyl, pyrazolo[4,3-c]pyridinyl, pyrazolo[3,4-c]pyridinyl, pyrazolo[3,4-b]pyridinyl, isoindolyl, indazolyl, purinyl, indolininyl, imidazo[1,2-a]pyridiny
  • heteroarylalkyl means alkyl substituted with a heteroaryl group.
  • heteroarylene includes divalent heteroaromatic, cyclic hydrocarbyl groups additionally containing one or more heteroatoms independently selected from O, S, N and NR N , where R N is defined below (and in one embodiment is H or alkyl (e.g. C 1-6 alkyl)).
  • R N is defined below (and in one embodiment is H or alkyl (e.g. C 1-6 alkyl)).
  • the heteroarylene groups may be monocyclic or polycyclic (e.g. bicyclic) fused ring heteroaromatic groups.
  • heteroarylene groups contain 5-13 ring members (preferably 5-10 members) and 1, 2, 3 or 4 ring heteroatoms independently selected from O, S, N and NR N .
  • a heteroarylene group may be 5, 6, 9 or 10 membered, e.g.
  • heteroarylene includes divalent derivatives of each of the heteroaryl groups discussed above.
  • aryl also include groups that are partially reduced.
  • heteroaryl includes fused species in which one of the rings has been reduced to a saturated ring (e.g., 1,2,3,4-tetrahydro-1,8-naphthyridin-2-yl).
  • R N is H or optionally substituted C 1-6 alkyl, C 1-6 heteroalkyl, C 3-6 cycloalkyl, C 3-6 heterocycloalkyl, C 2-6 alkenyl, C 2-6 heteroalkenyl, C 3-6 cycloalkenyl, C 3-6 heterocycloalkenyl, phenyl, or heteroaryl containing 5 or 6 ring members.
  • R N is preferably H, C 1-6 alkyl or C 3-6 cycloalkyl. q is independently 0, 1 or 2. In one embodiment, q is 0. r is independently 0 or 1. In one embodiment, r
  • heteroatom containing groups such as heteroalkyl etc.
  • a numerical of carbon atoms is given, for instance C 3-6 heteroalkyl
  • a C 3-6 heteroalkyl group would, e.g., contain less than 3-6 chain carbon atoms.
  • a pyridyl group would be classed as a C 6 heteroaryl group even though it contains 5 carbon atoms.
  • ether e.g., —O—
  • ester e.g., —C(O)O—
  • succinate e.g., —O(O)C—CH 2 —CH 2 —C(O)O—
  • carbamate e.g., —OC(O)—NR′—
  • carbonate e.g., —OC(O)O—
  • ketone e.g., —C—C(O)—C—
  • carbonyl e.g., —C(O)—
  • urea e.g., —NRC(O)NR′—
  • amine e.g., —NR′—
  • amide e.g., —C(O)NR′—
  • imine e.g., —C(NR′)—
  • thioether e.g., —S—
  • xanthate e.g., —OC(S)S—
  • 2 mM solution of lipid in ethanol are prepared by weighing the lipid and then dissolving in ethanol.
  • 0.3 mM solution of fluorescent probe TNS in ethanol:methanol 9:1 is prepared by first making 3 mM solution of TNS in methanol and then diluting to 0.3 mM with ethanol.
  • aqueous buffer containing sodium phosphate, sodium citrate sodium acetate and sodium chloride, at the concentrations 20 mM, 25 mM, 20 mM and 150 mM, respectively, is prepared.
  • the buffer is split into eight parts and the pH adjusted either with 12N HCl or 6N NaOH to 4.44-4.52, 5.27, 6.15-6.21, 6.57, 7.10-7.20, 7.72-7.80, 8.27-8.33 and 10.47-11.12. 400 uL of 2 mM lipid solution and 800 uL of 0.3 mM TNS solution are mixed.
  • probe/lipid mix 7.5 uL are added to 242.5 uL of buffer in a 1 mL 96 well plate (model NUNC 260252, Nalgae Nunc International). This is done with all eight buffers.
  • each probe/lipid/buffer mixture is transferred to a 250 uL black with clear bottom 96 well plate (model COSTAR 3904, Corning).
  • the fluorescence measurements are carried out on the SpectraMax M5 spectrophotometer using software SoftMax pro 5.2 and following parameters:
  • the background fluorescence value of an empty well on the 96 well plate is subtracted from each probe/lipid/buffer mixture.
  • the fluorescence intensity values are then normalized to the value at lowest pH.
  • the normalized fluorescence intensity vs. pH chart is then plotted in the Microsoft Excel software. The eight points are connected with a smooth line.
  • the point on the line at which the normalized fluorescence intensity is equal to 0.5 is found.
  • the pH corresponding to normalized fluorescence intensity equal to 0.5 is found and is considered the pKa of the lipid.
  • the pKa determined using this method is precise to about 0.2 pKa units.
  • group a, b or c in formula (I) is “absent”, what is meant is that a single bond is present instead, i.e. that the two groups either side of group a, b or c are directly bonded to each other.
  • the term “optionally substituted” as applied to any of an aryl, heteroaryl, cycloalkyl or heterocyclyl group refers to such a group that is unsubstituted or is substituted by one or more, typically 1, 2, 3, 4 or 5 suitable non-hydrogen substituents, each of which is independently selected from the group consisting of:
  • Groups of the compounds of the invention may be substituted or unsubstituted, in one embodiment unsubstituted.
  • substitution involves the notional replacement of a hydrogen atom with a substituent group, or two hydrogen atoms in the case of substitution by ⁇ O.
  • substituents on each group there will generally be 1 to 5 substituents on each group, in one embodiment 1 to 3 substituents, in one embodiment 1 or 2 substituents, in one embodiment 1 substituent.
  • One embodiment includes more than one substituent on the same atom, e.g. an acetal group.
  • the substituent(s) is/are independently Sub 1 or Sub 2 (in one embodiment Sub 2 ) wherein:
  • Sub 1 is independently Sub 1 is independently halogen, trihalomethyl, trihaloethyl, —NO 2 , —CN, —N + (R s ) 2 O ⁇ , —CO 2 H, —CO 2 R s , —SO 3 H, —SOR s , —SO 2 R s , —SO 3 R s , —OC( ⁇ O)OR s , —C( ⁇ O)H, —C( ⁇ O)R s , —OC( ⁇ O)R s , ⁇ O, —NR s 2 , —C( ⁇ O)NH 2 , —C( ⁇ O)NR s 2 , —N(R s )C( ⁇ O)OR s , —N(R s )C( ⁇ O)NR s 2 , —OC( ⁇ O)NR s 2 , —N(R s )C( ⁇ O)R s 2 , —OC
  • Sub 2 is independently halogen, trihalomethyl, trihaloethyl, —NO 2 , —CN, —N + (C 1-6 alkyl) 2 O ⁇ , —CO 2 H, —CO 2 C 1-6 alkyl, —SO 3 H, —SOC 1-6 alkyl, —SO 2 C 1-6 alkyl, —SO 3 C 1-6 alkyl, —OC( ⁇ O)OC 1-6 alkyl, —C( ⁇ O)H, —C( ⁇ O)C 1-6 alkyl, —OC( ⁇ O)C 1-6 alkyl, ⁇ O, —N(C 1-6 alkyl) 2 , —C( ⁇ O)NH 2 , —C( ⁇ O)N(C 1-6 alkyl) 2 , —N(C 1-6 alkyl)C( ⁇ O)C(C 1-6 alkyl), —N(C 1-6 alkyl)C( ⁇ O)N(C 1-6 alkyl) 2
  • R s in Sub 1 can be optionally substituted by 1 to 3 substituents Sub 2 , Sub 2 is unsubstituted. However, in one embodiment, R s is unsubstituted.
  • R s is H or C 1-6 alkyl, optionally substituted by 1 to 3 substituents Sub 2 .
  • Sub 2 is independently halogen, trihalomethyl, trihaloethyl, —NO 2 , —CN, —N + (C 1-6 alkyl) 2 O ⁇ , —CO 2 H, —SO 3 H, —SOC 1-6 alkyl, —SO 2 C 1-6 alkyl, —C( ⁇ O)H, —C( ⁇ O)C 1-6 alkyl, ⁇ O, —N(C 1-6 alkyl) 2 , —C( ⁇ O)NH 2 , —C 1-6 alkyl, —C 3-6 cycloalkyl, —C 3-6 heterocycloalkyl, —Z t —C 1-6 alkyl or —Z t —C 3-6 cycloalkyl.
  • Sub 1 is not —R s and Sub 2 is not —C 1-6 alkyl, —C 1-6 heteroalkyl, —C 2-6 alkenyl, —C 2-6 heteroalkenyl, —C 2-6 alkynyl or —C 2-6 heteroalkynyl.
  • a group other than Sub 2 has at least 2 positions which may be substituted
  • the group may be substituted by both ends of an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene chain (in one embodiment containing 1 to 6 atoms, in one embodiment 3 to 6 atoms, and in one embodiment 3 or 4 atoms) to form a cyclic moiety. That chain is optionally substituted by 1 to 3 substituents Sub 2 . In one embodiment that chain is not substituted.
  • cycloalkyl cycloalkenyl
  • cycloalkynyl cycloalkynyl
  • heterocycloalkyl cycloalkenyl
  • heterocycloalkynyl cycloalkynyl
  • aryl cycloaryl
  • heteroaryl includes a species in which a heterocycloalkyl ring is fused to the aromatic ring (e.g. 5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl).
  • a group other than Sub 2 has an atom which may be substituted twice, that atom may be substituted by both ends of an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene chain (in one embodiment containing 2 to 8 atoms, in one embodiment 3 to 6 atoms, and in one embodiment 4 or 5 atoms) to form a cyclic moiety. That chain is optionally substituted by 1 to 3 substituents Sub 2 . In one embodiment that chain is not substituted.
  • cycloalkyl optionally substituted “cycloalkyl”, “cycloalkenyl”, “cycloalkynyl”, “heterocycloalkyl”, “heterocycloalkenyl”, “heterocycloalkynyl”, “aryl” and “heteroaryl” include spiro species.
  • heteroalkyl when a group has a heteroatom, a substituent may be bonded to the heteroatom.
  • “optionally substituted heteroalkyl” includes —CH 2 —N(Sub 1 )-CH 2 —, —CH(Sub 1 )-NH—CH 2 — and —CH(Sub 1 )-N(Sub 1 )-CH 2 — etc.
  • the phrase “optionally substituted C 3-20 -heterocycloalkyl, C 3-20 -heterocycloalkenyl, C 3-20 -heterocycloalkynyl or C 5-20 -heteroaryl group” means that each of the four items in the list, namely the C 3-20 -heterocycloalkyl group, the C 3-20 -heterocycloalkenyl group, the C 3-20 -heterocycloalkynyl group and the C 6-20 -heteroaryl group, may be optionally substituted.
  • a group is characterised by a first modifier and then, later on, the same group is characterised by a subsequent modifier, what is meant is that the group is characterised by both modifiers simultaneously.
  • a group is described as a “C 3-20 -heterocycloalkynyl” (the first modifier) group and then later the same group is described as a “C 5-16 ” (the subsequent modifier) group, what is meant is a C 5-16 heterocycloalkynyl group.
  • steroid refers to any group comprising the following structure (which structure is referred to herein as the “steroid skeleton”).
  • the steroid skeleton has been drawn, above as fully saturated.
  • the term steroid is also intended to cover instances where there is unsaturation in the steroid skeleton.
  • the term steroid covers a group which comprises the fully unsaturated (mancude) basic skeleton, 15H-cyclopenta[a]phenanthrene:
  • steroid also covers a group which comprises a partially unsaturated steroid skeleton.
  • steroid also covers “seco” derivatives of the steroid skeleton, i.e. groups in which ring cleavage has been effected; “nor” and “homo” derivatives of the steroid skeleton which involve ring contraction and expansion, respectively (see Systemic Nomenclature of Organic Chemistry, by D. Hellwinkel, published by Springer, 2001, ISBN: 3-540-41138-0, page 203 for “seco” and page 204 for “nor” and “homo”). In one embodiment, however, such “seco” derivatives are not encompassed by the term “steroid”. In another embodiment, such “nor” derivatives are not encompassed by the term “steroid”. In another embodiment, such “homo” derivatives are not encompassed by the term “steroid”. Thus in one embodiment, such seco, nor and homo derivatives are not encompassed by the term “steroid”.
  • steroid also covers instances where one or more of the carbon atoms in the structure labelled steroid skeleton is replaced by a heteroatom.
  • up to six carbon atoms in one embodiment up to five carbon atoms, in another embodiment up to four carbon atoms, in another embodiment up to three carbon atoms, in another embodiment up to two carbon atoms, in another embodiment one carbon atom, are each replaced independently by O, S(O) q , N, P(O) r or Si (and preferably O, S(O) q or N).
  • the term “steroid” comprises species in which the “steroid basic skeleton” contains no heteroatoms.
  • a steroid ring system is numbered according to the convention set out below.
  • steroid encompasses sterols, steroid hormones, bile acids and salts of bile acids.
  • a sterol is any steroid with a hydroxyl group at the 3-position of the A-ring.
  • the omega-3 position refers to the third bond from the (methyl) terminal of the chain; the omega-6 position refers to the sixth bond from the (methyl) terminal of the chain and the omega-9 position refers to the ninth bond from the (methyl) terminal of the chain.
  • PDI polydispersity index. Unless indicated otherwise, all PDIs referred to herein are the PDI of the fully formed nanoparticle, as measured by dynamic light scattering on a Malvern Zetasizer.
  • the nanoparticle sample is diluted in phosphate buffered saline (PBS) so that the count rate is approximately 200-400 kcts.
  • PBS phosphate buffered saline
  • composition “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.
  • Route A sets out a general method which can be used to synthesise compounds of the invention.
  • Route CDT illustrates how the cholesterol diglycol tosylate reagent might be prepared.
  • Linoleyl alcohol (48.7 g, 183 mmol) is added to a round bottom flask and dissolve in THF (400 mL). The resulting solution is cooled using an ice bath and sodium hydride (13.16 g, 329 mmol) is added. The resulting slurry is stirred for 1 h at rt. Epibromohydrin is added in one portion and the reaction is continued at rt. After 4 h stirring, additional sodium hydride (13.16 g, 329 mmol) is added. After an additional h stirring at rt, another aliquot of epibromohydrin (32.5 g, 238 mmol) is added. The reaction is then heated to 50° C. overnight.
  • Cholesterol (50 g, 129 mmol) is dissolved in DCM (55 mL) and pyridine (150 mL). The resulting solution is cooled to 0° C. and tosyl chloride is added in one portion as a solid. The reaction is allowed to slowly warm to rt overnight. The reaction is concentrated by rotary evaporation and MeOH (500 mL) is added to produce a white solid. Stirring is continued for 30 min and the precipitate collected by filtration, washed with MeOH and dried under vacuum to yield the desired tosylate.
  • Cholesterol tosylate (73 g, 128 mmol) is dissolved in 1,4-dioxane (750 mL). Diethylene glycol (294 mL, 3077 mmol) is added and the reaction is heated to a gentle reflux overnight. The resulting solution is cooled to rt and concentrated by rotary evaporation. The resulting gel is taken up in DCM and stirred with water. The resulting organic layer is collected and the aqueous layer extracted once with DCM. The organic layers are combined, dried over sodium sulfate, and concentrated by rotary evaporation. The crude product is purified on silica in EtOAc/heptane to yield the desired cholesterol diglycol.
  • Example 5 The amino alcohol from Example 5 (0.447 mg, 1.09 mmol) is stirred in toluene (15 mL) and NaH (0.102 g, 4.24 mmol) is added in one portion. The resulting mixture is stirred at rt for 30 min and the tosylate from Example 4 is added in one portion. The reaction is heated to reflux overnight. After cooling to room temperature (“rt”), the reaction is quenched by the addition of saturated aqueous sodium bicarbonate. The resulting mixture is stirred for 5 min and then concentrated by rotary evaporation. The resulting residue is purified directly on silica in MeOH/DCM to yield a crude product that is repurified on silica in EtOAc/heptane to yield the desired compound.
  • Route B also represents a general method which can be used to synthesise compounds of the invention.
  • the reaction mixture is concentrated, and the residue is purified by flash chromatography on an IntelliFlash 280 (AnaLogix) using a SF40-80G column: 0-2 CV, 100% CH 2 Cl 2 ; 2-10 CV, linear gradient of 100:0 CH 2 Cl 2 :(MeOH 10% AcOH) to 90:10 CH 2 Cl 2 :(MeOH 10% AcOH); 10-25 CV, linear gradient of 90:10 CH 2 Cl 2 :(MeOH 10% AcOH) to 85:15 CH 2 Cl 2 :(MeOH 10% AcOH).
  • the product co-elutes with cholesterol.
  • the product-containing fractions are combined and concentrated in vacuo to a white slurry, then diluted with heptanes (cholesterol is soluble in heptanes) and chilled in an ice bath. The white solid is filtered off, washed with heptanes, and placed under vacuum, yielding 1.50 g (35%) of pure product.
  • the crude reaction mixture is purified via flash chromatography on an IntelliFlash 280 (AnaLogix) using a SF15-24G column: 0-3 CV, 100% CH 2 Cl 2 ; 3-25 CV, linear gradient of 100:0 CH 2 Cl 2 :MeOH to 95:5 CH 2 Cl 2 :MeOH.
  • the product is still impure.
  • the residue is purified again via flash chromatography on an IntelliFlash 280 (AnaLogix) using a SF15-24G column. 0-3 CV, 100% heptanes; 3-30 CV, linear gradient of 100:0 heptanes:ethyl acetate to 65:35 heptanes:ethyl acetate.
  • the product-containing fractions are identified by TLC, combined, and concentrated in vacuo to yield 38 mg (13%) of pure product as a clear liquid.
  • Route C also represents a general method which can be used to synthesise compounds of the invention.
  • 2-(2-Chloroethoxyethanol) (5.01 g, 40.2 mmol) is weighed into a round bottomed flask and dissolve in DMF (100 ml). The solution is stirred, NaN 3 (2.89 g, 44.5 mmol) is added, and the temperature is increased to 80° C. The solution became cloudy. The reaction is stirred overnight.
  • the reaction is diluted with CH 2 Cl 2 (50 mL) and extracted with 1M HCl (2 ⁇ 40 mL) to remove the pyridine.
  • the organic phase is washed once with brine (40 mL) and concentrated.
  • the residue is purified via flash chromatography on InternFlash 280 (AnaLogix) using a SF40-115G column: 0-20 CV, linear gradient of 100:0 heptanes:ethyl acetate to 50:50 heptanes:ethyl acetate.
  • the product containing fractions are identified by TLC, combined, and concentrated in vacuo to yield the product with an estimated 90% purity: 0.61 g (10%).
  • the alkylazide from example 11 (334 mg, 0.641 mmol) is dissolved in THF (4 mL) and water (0.400 mL) in a small vial. To this solution is added a solution of trimethylphosphine in THF (2.5 mL, 2.500 mmol trimethylphosphine) and the reaction is stirred overnight. The reaction appears complete by TLC the next morning. The solvent is evaporated and the residue is dissolved in 10 mL MeOH. The solution is loaded onto a SCX (10 g) column preequilibrated with MeOH, washed with 50 mL MeOH, then elutes with 4 ⁇ 10 mL 7M NH 3 in MeOH.
  • the crude reaction mixture is purified directly via flash chromatography on an IntelliFlash 280 (AnaLogix) using a SF15-24G column: 0-5 CV, 100% CH 2 Cl 2 ; 5-15 CV, linear gradient of 100:0 CH 2 Cl 2 :MeOH to 95:5 CH 2 Cl 2 :MeOH; 15-30, 95:5 CH 2 Cl 2 :MeOH.
  • the product containing fractions are identified by TLC, combined, and concentrated to a pale yellow oil: 339 mg (80%).
  • Route D also represents a general method which can be used to synthesize compounds of the invention
  • the reaction is extracted between a saturated aqueous solution of NaHCO 3 and ethyl acetate.
  • the organic extracts are combined, dried and concentrated.
  • the residue is purified via flash chromatography eluting with 30% ethyl acetate/70% heptane: 5.45 g (63%).
  • Route E also represents a general method which can be used to synthesise compounds of the invention.
  • a 1N solution of aqueous HCl (0.38 mL, 0.38 mmol) is added dropwise to a solution of the vinyl ether from example 17 (100 mg, 0.19 mmol) in 4 mL of 1:1 ethanol/THF at rt. After 1 h, the reaction is extracted between a saturated aqueous solution of NaHCO 3 and ethyl acetate. The organic extracts are combined, dried and concentrated to an oil that is used in the next step without further purification: 85 mg (90%).
  • Route F also represents a general method which can be used to synthesise compounds of the invention.
  • the reaction mixture is cooled and extracted between brine and ethyl acetate.
  • the organic extracts are combined, dried with Na 2 SO 4 , and concentrated to an oil.
  • the crude oil is purified via flash chromatography with 5% MeOH/95% CH 2 Cl 2 : 720 mg (66%).
  • Route G also represents a general method which can be used to synthesise compounds of the invention.
  • the material from example 21 is stirred in ethanol (25 mL) and a solution of methylamine in THF is added. The reaction is stirred at rt for 16 h and then concentrated to dryness. The crude material is purified by chromatography on silica.
  • Route H also represents a general method which can be used to synthesise compounds of the invention.
  • E0102 can be prepared using the Route H methodology.
  • Route I also represents a general method which can be used to synthesise compounds of the invention.
  • E0110 and E0111 can be prepared using the Route I methodology.
  • Examples 28 to 32 also represent routes which can be used to synthesise compounds of the invention.
  • BOC protected cationic lipid prepared using Route A methodology (150 mg) is stirred with triethylsilane (0.5 mL) and TFA (10 mL) is added in one portion. After 2 h, the reaction is concentrated to dryness. The resulting residue is purified on silica on 0 to 15% MeOH in DCM and concentrated to a glassy oil.
  • E0012 can be made using this process.
  • TBDMS protected cationic lipid prepared using Route A methodology (135 mg, 0.138 mmol) is stirred in THF (2 mL) and a solution of TBAF (0.28 mL, 1.0 M in THF, 0.28 mmol) is added. The reaction is stirred at rt overnight. The reaction is purified directly on silica in 0 to 20% MeOH in DCM to yield a clear oil.
  • Examples 30 to 31 also represent routes which can be used to synthesise compounds of the invention.
  • the starting material for making E0115, E0116, E0117 and E0160 can be made using steps from Example 30 and this Example 31.
  • Ethylene glycol (0.30 g) is stirred in THF (20 mL) and 60 wt % sodium hydride is added (0.19 g). The resulting mixture is stirred for 20 min. Linoleyl mesylate (1.64 g) is added and the reaction is heated to 50° C. for 2 h and then to reflux overnight. The reaction is cooled to rt and stirred for an additional 24 h. To the reaction is added saturated aqueous ammonium chloride and the resulting mixture is extracted with DCM. The resulting organic layer is dried over sodium sulfate and concentrated to a crude oil. The crude material is purified on silica using EtOAc in heptanes to yield 640 mg of the desired product.
  • examples 30 to 32 may be used in the synthesis of lipids (e.g. E0055) having a spacer between the linoleyl chains and the core of the molecule.
  • lipids e.g. E0055
  • Route J also represents a general method which can be used to synthesise compounds of the invention.
  • Route K also represents a general method which can be used to synthesise compounds of the invention.
  • Example 36 The compound from Example 36 (2.6 g) is stirred in DCM (10 mL) and TFA (10 mL) is added. After 3 h, the reaction is concentrated to dryness and used directly in the next step.
  • Route L also represents a general method which can be used to synthesise compounds of the invention.
  • the alcohol (1.3 g, 2.9 mmol) is stirred in MePh (10 mL). NaH is added (0.46 g, 11.4 mmol) and the reaction is stirred at rt for 30 min.
  • the compound from Example 39 (1.7 g, 1.2 mmol) is added and the reaction is stirred for 16 h at rt.
  • the reaction is cooled in an ice bath and quenched with water.
  • the resulting mixture is extracted with EtOAc.
  • the organic layers are combined, washed with brine, dried over sodium sulfate and concentrated to a crude oil.
  • the material is purified on silica in EtOAc/hexane to yield 1 g of the desired product.
  • E0146 can be made using Route L technology.
  • Examples 41, 42 and 43 are reserved and are purposefully left blank.
  • Route X also represents a general method that can be used to synthesise compounds of the invention.
  • E0180 can be manufactured by the Route X methodology
  • Route Y also represents a general method that can be used to synthesise compounds of the invention.
  • E0167 can be manufactured using route Y methodology.
  • the structures of the stealth lipids S001 through S026 are provided in Table 3.
  • the following examples 54 to 67 illustrate the synthesis of stealth lipids.
  • Stealth lipid structures Stealth Lipid Lipid S001 S002 S003 S004 S005 S006 S007 S008 S009 S010 S011 S012 S013 S014 S015 S016 S017 S018 S019 S020 S021 S022 S023 S024 S025 S026
  • ⁇ -alanine hydrochloride (1.00 g, 7.16 mmol), cholesterol chloroformate (3.06 g, 6.81 mmol) and triethylamine (2.0 ml, 14 mmol) are dissolved in anhydrous chloroform (25 ml). The solution is stirred at rt overnight. The next morning, the solvent is evaporated and the residue is dissolved in ethyl acetate (100 mL) and washed with 1 M HCl, brine, and dried with Na 2 SO 4 . The product is concentrated to a white solid and used in the next step without further purification: 3.31 g, 90.0%.
  • N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (96 mg, 0.50 mmol), the product (carboxylic acid) from the previous step (252 mg, 0.477 mmol), N,N-dimethylaminopyridine (122 mg, 1.00 mmol) and poly(ethylene glycol) methyl ether (200 mg, 0.100 mmol, M n ⁇ 2,000 g/mol, Sigma-Aldrich) are dissolved in anhydrous dichloromethane (5.0 mL) and stirred at rt.
  • the reaction mixture is loaded onto a 10 g Bond Elut SCX column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol) and elutes with 50:50 dichloromethane:methanol.
  • the product containing fractions are identified by TLC, combined, and concentrated.
  • the crude product is further purified by flash chromatography on silica with a dichloromethane/methanol gradient.
  • the product containing fractions are identified by TLC, combined and concentrated to a white solid: 151 mg, 60.3%.
  • PEG-NH 2 500 mg, 0.250 mmol, M n ⁇ 2000 g/mol, “Sunbright MEPA-20H”, NOF Corp.
  • cholesterol chloroformate 449 mg, 1.00 mmol
  • N,N-dimethylaminopyridine 122 mg, 1.00 mmol
  • N,N-diisopropylethylamine 148 mg, 1.15 mmol
  • the reaction mixture is loaded onto a 10 g Bond Elut SCX column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol) and elutes with 50:50 dichloromethane:methanol.
  • the product containing fractions are identified by TLC, combined, and concentrated.
  • the crude product is further purified by flash chromatography on silica with a dichloromethane/methanol gradient.
  • the product containing fractions are identified by TLC, combined and concentrated to a white solid: 376 mg, 57.8%.
  • the solution is diluted with dichloromethane and washed with water, 0.1 M NaOH, 1 M HCl, and brine.
  • the organic phase is dried with sodium sulfate and filtered.
  • the crude material is crystallized twice from hot heptane, yielding the product as a white powder: 195 mg, 20.0%.
  • the product (4-nitrophenyl carbonate) from the previous step is dissolved in toluene (5 ml) at rt.
  • PEG-NH 2 800 mg, 0.400 mmol, M n ⁇ 2000 g/mol, “Sunbright MEPA-20H”, NOF Corp.
  • N,N-dimethylaminopyridine 50 mg, 0.409 mmol
  • N,N-diisopropylethylamine 200 ⁇ l, 1.145 mmol
  • the product (4-nitrophenyl carbonate) from the previous step (260 mg, 0.386 mmol) is dissolved in toluene (4 mL), followed by PEG2k (620 mg, 0.310 mmol, M n ⁇ 2000 g/mol, “Sunbright MEPA-20H”, NOF Corp.), N,N-dimethylaminopyridine (40 mg, 0.33 mmol), and N,N-diisopropylethylamine (200 ⁇ l, 1.15 mmol). The solution is stirred at rt overnight.
  • the reaction mixture is loaded onto a 10 g Bond Elut SCX column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol) and elutes with 50:50 dichloromethane:methanol.
  • the product containing fractions are identified by TLC, combined, and concentrated.
  • the crude product is further purified by flash chromatography on silica with a dichloromethane/methanol gradient.
  • the product containing fractions are identified by TLC, combined and concentrated.
  • To remove 4-nitrophenol impurities the crude product is dissolved in 1:1 dichloromethane:methanol and elutes through a 10 g Bond Elut NH2 column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol).
  • the product containing fractions are identified by TLC, combined, and concentrated to a pale yellow solid: 631 mg, 78.0%.
  • the product (alcohol) from the previous step (310 mg, 0.664 mmol) is dissolved in dichloromethane (15 mL). Pyridine (0.134 mL, 1.66 mmol) is then added, followed by 4-nitrophenyl chloroformate (167 mg, 0.830 mmol). The reaction is stirred overnight at rt. The reaction is diluted with ethyl acetate, washed with a saturated aqueous solution of NaHCO 3 , dried with sodium sulfate, and concentrated. The crude product is further purified by flash chromatography on silica with a heptane/ethyl acetate gradient. The product containing fractions are identified by TLC, combined and concentrated: 315 mg, 75.0%.
  • the reaction mixture is loaded onto a 10 g Bond Elut SCX column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol) and elutes with 50:50 dichloromethane:methanol.
  • the product containing fractions are identified by TLC, combined, and concentrated.
  • the crude product is further purified by flash chromatography on silica with a dichloromethane/methanol gradient.
  • the product containing fractions are identified by TLC, combined and concentrated: 540 mg, 54.3%.
  • the product (alcohol) from the previous step (200 mg, 0.404 mmol) is dissolved in dichloromethane (6 mL). Pyridine (0.082 mL, 1.01 mmol) is then added, followed by 4-nitrophenyl chloroformate (102 mg, 0.505 mmol). The reaction is stirred overnight at rt. The reaction is diluted with ethyl acetate, washed with a saturated aqueous solution of NaHCO 3 , dried with sodium sulfate, and concentrated. The crude product is further purified by flash chromatography on silica with a heptane/ethyl acetate gradient. The product containing fractions are identified by TLC, combined and concentrated: 220 mg, 82.0%.
  • the reaction mixture is loaded onto a 10 g Bond Elut SCX column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol) and elutes with 50:50 dichloromethane:methanol.
  • the product containing fractions are identified by TLC, combined, and concentrated.
  • the crude product is further purified by flash chromatography on silica with a dichloromethane/methanol gradient.
  • the product containing fractions are identified by TLC, combined and concentrated: 600 mg, 68.3%.
  • S009 may be prepared in a manner analogous to that described for S008.
  • S010 and S011 may be prepared, e.g., as provided in PCT publication WO2009086558 compounds IVa and IVc, respectively. These compounds may be synthesized as provided in Example 19 of WO2009086558.
  • S012 may be prepared in a manner analogous to that described for S001, utilizing PEG-NH 2 (“Sunbright MEPA-20H”, NOF Corp.) instead of poly(ethylene glycol) methyl ether.
  • S006, S013, S014, S015, S016, S017, S018, S019, S020, S021, S022, S023, and S024 may be prepared in a manner analogous to that described for S004.
  • the reaction mixture is loaded onto a 10 g Bond Elut SCX column (from Varian; pre-equilibrated with 50:50 dichloromethane:methanol) and elutes with 50:50 dichloromethane:methanol.
  • the product containing fractions are identified by TLC, combined, and concentrated.
  • the crude product is further purified by flash chromatography on silica with an ethyl acetate/heptane gradient.
  • the product containing fractions are identified by TLC, combined and concentrated to a white solid: 131 mg, 44%.
  • Table 6 provides the structures of the cationic lipids of the invention.
  • Y 2 is cholesterol linked to L via an oxygen atom on the 3-position of the A steroid ring (the hydrogen atom on said hydroxy group being absent);
  • X 1 and X 2 are O;
  • a methylene;
  • 1 H NMR is taken of all lipids to assess purity and any olefin isomerization that may have occurred in the synthesis.
  • the integrals for the cholesterol derived singlet is compared to the olefin derived signals in the 5.2 to 5.5 ppm range.
  • the olefin integral for the desired cis, unconjugated olefins and the cholesterol olefinic hydrogen is compared to any new signals above 5.5 ppm which corresponded to isomerized products. In all cases, the degree of isomerization is less than 10% as determined by comparing the integrated signals in the 1 H NMR.
  • ELSD detector *6 - Zorbax Eclipse XDB-C18 250 ⁇ 4.6, 1 mL/min, water:MeOH w/0.1% TFA, 50% for 5 min, then 50 to 100% over 5 min, then hold at 100% for 5 min, ELSD detector.
  • compositions of the invention comprise lipid nanoparticles which comprise the compounds of the invention and optionally one or more other lipid components.
  • the skilled person may use the method steps set out below, experimenting with different combinations. Additionally, the skilled person could employ sonication, filtration or other sizing techniques which are used in liposomal formulations.
  • the process for making a composition of the invention typically comprises providing an aqueous solution comprising a biologically active agent in a first reservoir, providing a second reservoir comprising an organic solution of the lipid(s) and then mixing the aqueous solution with the organic lipid solution.
  • the first reservoir is optionally in fluid communication with the second reservoir.
  • the mixing step is optionally followed by an incubation step, a filtration step, and a dilution and/or concentration step.
  • the biologically active agent(s) and/or the lipid(s) is/are in a suitable buffer.
  • the biologically active agent(s) is in an aqueous buffer such as a citrate buffer.
  • the lipid(s) is in an organic alcohol such as ethanol.
  • the incubation step comprises allowing the solution from the mixing step to stand in a vessel for about 0 to about 100 hours (preferably about 0 to about 24 hours) at about rt and optionally protected from light.
  • a dilution step follows the incubation step.
  • the dilution step may involve dilution with aqueous buffer (e.g. citrate buffer) e.g., using a pumping apparatus (e.g. a peristaltic pump).
  • aqueous buffer e.g. citrate buffer
  • a pumping apparatus e.g. a peristaltic pump
  • the filtration step is ultrafiltration.
  • the ultrafiltration comprises concentration of the diluted solution followed by diafiltration, e.g., using a suitable pumping system (e.g. pumping apparatus such as a peristaltic pump or equivalent thereof) in conjunction with a suitable ultrafiltration membrane (e.g. GE Hollow fiber cartridges or equivalent).
  • a suitable pumping system e.g. pumping apparatus such as a peristaltic pump or equivalent thereof
  • a suitable ultrafiltration membrane e.g. GE Hollow fiber cartridges or equivalent.
  • the process should result in the formation of lipid nanoparticles.
  • the lipid nanoparticles comprise the biologically active agent.
  • the mixing step provides a clear single phase.
  • the organic solvent is removed to provide a suspension of particles, wherein the biologically active agent is encapsulated by the lipid(s), e.g. in a lipid bilayer.
  • organic solvent will typically involve consideration of solvent polarity and the ease with which the solvent can be removed at the later stages of particle formation.
  • the organic solvent which is also used as a solubilizing agent, is preferably in an amount sufficient to provide a clear single phase mixture of biologically active agents and lipids.
  • the organic solvent may be selected from one or more (e.g. two) of chloroform, dichloromethane, diethylether, cyclohexane, cyclopentane, benzene, toluene, methanol, and other aliphatic alcohols (e.g. C 1 to C 8 ) such as ethanol, propanol, isopropanol, butanol, tert-butanol, iso-butanol, pentanol and hexanol.
  • chloroform chloroform
  • dichloromethane diethylether
  • cyclohexane cyclopentane
  • benzene toluene
  • methanol methanol
  • other aliphatic alcohols e.g. C 1 to C 8
  • the mixing step can take place by any number of methods, e.g., by mechanical means such as a vortex mixer.
  • the methods used to remove the organic solvent will typically involve diafilitration or evaporation at reduced pressures or blowing a stream of inert gas (e.g. nitrogen or argon) across the mixture.
  • inert gas e.g. nitrogen or argon
  • the method further comprises adding nonlipid polycations which are useful to effect the transformation of cells using the present compositions.
  • suitable nonlipid polycations include, but are limited to, hexadimethrine bromide (sold under the brandname POLYBRENE®, from Aldrich Chemical Co., Milwaukee, Wis., USA) or other salts of hexadimethrine.
  • Other suitable polycations include, e.g., salts of poly-L-ornithine, poly-L-arginine, poly-L-lysine, poly-D-lysine, polyallylamine and polyethyleneimine.
  • the formation of the lipid nanoparticles can be carried out either in a mono-phase system (e.g. a Bligh and Dyer monophase or similar mixture of aqueous and organic solvents) or in a two-phase system with suitable mixing.
  • a mono-phase system e.g. a Bligh and Dyer monophase or similar mixture of aqueous and organic solvents
  • a two-phase system with suitable mixing.
  • the lipid nanoparticle may be formed in a mono- or a bi-phase system.
  • a mono-phase system the cationic lipid(s) and biologically active agent are each dissolved in a volume of the mono-phase mixture. Combining the two solutions provides a single mixture in which the complexes form.
  • the cationic lipids bind to the biologically active agent (which is present in the aqueous phase), and “pull” it into the organic phase.
  • the lipid nanoparticles are prepared by a method which comprises: (a) contacting the biologically active agent with a solution comprising noncationic lipids and a detergent to form a compound-lipid mixture; (b) contacting cationic lipids with the compound-lipid mixture to neutralize a portion of the negative charge of the biologically active agent and form a charge-neutralized mixture of biologically active agent and lipids; and (c) removing the detergent from the charge-neutralized mixture.
  • the solution of neutral lipids and detergent is an aqueous solution.
  • Contacting the biologically active agent with the solution of neutral lipids and detergent is typically accomplished by mixing together a first solution of the biologically active agent and a second solution of the lipids and detergent.
  • the biologically active agent solution is also a detergent solution.
  • the amount of neutral lipid which is used in the present method is typically determined based on the amount of cationic lipid used, and is typically of from about 0.2 to 5 times the amount of cationic lipid, preferably from about 0.5 to about 2 times the amount of cationic lipid used.
  • the biologically active agent-lipid mixture thus formed is contacted with cationic lipids to neutralize a portion of the negative charge which is associated with the molecule of interest (or other polyanionic materials) present.
  • the amount of cationic lipids used is typically the amount sufficient to neutralize at least 50% of the negative charge of the biologically active agent.
  • the negative charge will be at least 70% neutralized, more preferably at least 90% neutralized.
  • the methods used to remove the detergent typically involve dialysis. When organic solvents are present, removal is typically accomplished by diafilitration or evaporation at reduced pressures or by blowing a stream of inert gas (e.g. nitrogen or argon) across the mixture.
  • inert gas e.g. nitrogen or argon
  • the apparatus typically includes a first reservoir for holding an aqueous solution comprising a biologically active agent and a second reservoir for holding an organic lipid solution.
  • the apparatus also typically includes a pump mechanism configured to pump the aqueous and the organic lipid solutions into a mixing region or mixing chamber at substantially equal flow rates.
  • the mixing region or mixing chamber comprises a T coupling or equivalent thereof, which allows the aqueous and organic fluid streams to combine as input into the T connector and the resulting combined aqueous and organic solutions to exit out of the T connector into a collection reservoir or equivalent thereof.

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