WO2008083248A2 - Cyclopamine analogs - Google Patents

Cyclopamine analogs Download PDF

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Publication number
WO2008083248A2
WO2008083248A2 PCT/US2007/088990 US2007088990W WO2008083248A2 WO 2008083248 A2 WO2008083248 A2 WO 2008083248A2 US 2007088990 W US2007088990 W US 2007088990W WO 2008083248 A2 WO2008083248 A2 WO 2008083248A2
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WO
WIPO (PCT)
Prior art keywords
alkyl
compound
independently
aryl
aralkyl
Prior art date
Application number
PCT/US2007/088990
Other languages
French (fr)
Other versions
WO2008083248A3 (en
Inventor
Brian Austad
Somarajannair Janardanannair
Andre Lescarbeau
Martin Tremblay
Mark L. Behnke
Alfredo C. Castro
Andre B. Charette
Michael J. Grogan
Stephane Peluso
Original Assignee
Infinity Discovery, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to KR1020097015913A priority Critical patent/KR101489394B1/en
Priority to EP07870001.0A priority patent/EP2096917B1/en
Priority to NO20190059A priority patent/NO347310B1/en
Priority to CA2673995A priority patent/CA2673995C/en
Priority to AU2007339782A priority patent/AU2007339782B2/en
Priority to JP2009544276A priority patent/JP5412292B2/en
Priority to UAA200907837A priority patent/UA97130C2/en
Priority to NZ577916A priority patent/NZ577916A/en
Priority to MX2009007077A priority patent/MX2009007077A/en
Priority to CN200780051114.7A priority patent/CN101631463B/en
Application filed by Infinity Discovery, Inc. filed Critical Infinity Discovery, Inc.
Priority to ES07870001.0T priority patent/ES2488466T3/en
Priority to RU2009128997/04A priority patent/RU2486194C2/en
Priority to DK07870001.0T priority patent/DK2096917T3/en
Priority to BRPI0720972A priority patent/BRPI0720972B8/en
Priority to MX2012007856A priority patent/MX342683B/en
Priority to PL07870001T priority patent/PL2096917T3/en
Publication of WO2008083248A2 publication Critical patent/WO2008083248A2/en
Publication of WO2008083248A3 publication Critical patent/WO2008083248A3/en
Priority to ZA2009/04445A priority patent/ZA200904445B/en
Priority to IL199554A priority patent/IL199554B/en
Priority to NO20092710A priority patent/NO343748B1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D491/00—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00
    • C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
    • C07D491/10—Spiro-condensed systems
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    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/4353—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/4355—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems the heterocyclic ring system containing a five-membered ring having oxygen as a ring hetero atom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/4747—Quinolines; Isoquinolines spiro-condensed
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    • A61K31/16—Amides, e.g. hydroxamic acids
    • A61K31/17—Amides, e.g. hydroxamic acids having the group >N—C(O)—N< or >N—C(S)—N<, e.g. urea, thiourea, carmustine
    • A—HUMAN NECESSITIES
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    • A61K31/185—Acids; Anhydrides, halides or salts thereof, e.g. sulfur acids, imidic, hydrazonic or hydroximic acids
    • A61K31/19—Carboxylic acids, e.g. valproic acid
    • A61K31/195—Carboxylic acids, e.g. valproic acid having an amino group
    • A61K31/196—Carboxylic acids, e.g. valproic acid having an amino group the amino group being directly attached to a ring, e.g. anthranilic acid, mefenamic acid, diclofenac, chlorambucil
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    • A61K31/19—Carboxylic acids, e.g. valproic acid
    • A61K31/195—Carboxylic acids, e.g. valproic acid having an amino group
    • A61K31/197—Carboxylic acids, e.g. valproic acid having an amino group the amino and the carboxyl groups being attached to the same acyclic carbon chain, e.g. gamma-aminobutyric acid [GABA], beta-alanine, epsilon-aminocaproic acid or pantothenic acid
    • A61K31/198—Alpha-amino acids, e.g. alanine or edetic acid [EDTA]
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    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445—Non condensed piperidines, e.g. piperocaine
    • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
    • A61K31/454—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
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    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/4738—Quinolines; Isoquinolines ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/4741—Quinolines; Isoquinolines ortho- or peri-condensed with heterocyclic ring systems condensed with ring systems having oxygen as a ring hetero atom, e.g. tubocuraran derivatives, noscapine, bicuculline
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    • A61K31/4745—Quinolines; Isoquinolines ortho- or peri-condensed with heterocyclic ring systems condensed with ring systems having nitrogen as a ring hetero atom, e.g. phenantrolines
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    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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    • A61K31/56—Compounds containing cyclopenta[a]hydrophenanthrene ring systems; Derivatives thereof, e.g. steroids
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    • A61K31/56—Compounds containing cyclopenta[a]hydrophenanthrene ring systems; Derivatives thereof, e.g. steroids
    • A61K31/57—Compounds containing cyclopenta[a]hydrophenanthrene ring systems; Derivatives thereof, e.g. steroids substituted in position 17 beta by a chain of two carbon atoms, e.g. pregnane or progesterone
    • A61K31/573—Compounds containing cyclopenta[a]hydrophenanthrene ring systems; Derivatives thereof, e.g. steroids substituted in position 17 beta by a chain of two carbon atoms, e.g. pregnane or progesterone substituted in position 21, e.g. cortisone, dexamethasone, prednisone or aldosterone
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    • A61K31/56—Compounds containing cyclopenta[a]hydrophenanthrene ring systems; Derivatives thereof, e.g. steroids
    • A61K31/58—Compounds containing cyclopenta[a]hydrophenanthrene ring systems; Derivatives thereof, e.g. steroids containing heterocyclic rings, e.g. danazol, stanozolol, pancuronium or digitogenin
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    • A61K31/7028—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages
    • A61K31/7034—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages attached to a carbocyclic compound, e.g. phloridzin
    • A61K31/704—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages attached to a carbocyclic compound, e.g. phloridzin attached to a condensed carbocyclic ring system, e.g. sennosides, thiocolchicosides, escin, daunorubicin
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    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
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    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
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    • A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
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    • C07D307/94—Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom spiro-condensed with carbocyclic rings or ring systems, e.g. griseofulvins
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    • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
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    • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
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    • C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
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    • C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
    • C07D491/04—Ortho-condensed systems
    • C07D491/044—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring
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    • C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
    • C07D491/10—Spiro-condensed systems
    • C07D491/107—Spiro-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring
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    • C07—ORGANIC CHEMISTRY
    • C07J—STEROIDS
    • C07J69/00—Steroids in which the cyclopenta(a)hydrophenanthrene skeleton has been modified by contraction of only one ring by one atom and expansion of only one ring by one atom

Definitions

  • the present invention generally relates to cyclopamine analogs and pharmaceutical compositions thereof, and methods for preparing such analogs and compositions. These compounds and compositions are useful for the treatment of disorders mediated by the hedgehog pathway, such as cancer.
  • Inhibition of the hedgehog pathway in certain cancers has been shown to result in inhibition of tumor growth.
  • anti-hedgehog antibodies have been shown to antagonize the function of the hedgehog pathway and inhibit the growth of tumors.
  • Small molecule inhibition of hedgehog pathway activity has also been shown to result in cell death in a number of cancer types.
  • PCT publication WO 2006/026430 published 9 March 2006 and assigned to the same assignee as the present application, discloses a wide variety of cyclopamine analogs, focusing on those with unsaturation in the A or B ring.
  • the surprisingly potent analogs contain completely saturated A and B rings.
  • the present invention relates to analogs of steroidal alkaloids, such as cyclopamine, pharmaceutical compositions containing these compounds, and methods for preparing these compounds.
  • the present invention relates to a compound represented by the following structure: or a pharmaceutically acceptable salt thereof; wherein R 1 is H, alkyl, -OR, amino, sulfonamido, sulfamido, -OC(O)R 5 , - N(R 5 )C(O)R 5 , or a sugar;
  • R 3 is H, alkyl, alkenyl, or alkynyl
  • R 4 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR 5 , -C(O)R 5 , -CO 2 R 5 , -SO 2 R 5 , -C(O)N(R 5 )(R 5 ), -[C(R) 2 ] q -R 5 , -[(W)-N(R)C(0)] q R 5 , -[(W)-C(0)] q R 5 , -[(W)-C(0)0] q R 5 , -[(W)-0C(0)] q R 5 , -[(W)-SO 2 ] q R 5 , -[(W)-N(R 5 )SO 2 ] q R 5 , -[(W)-C(O)N(R 5
  • each R 5 is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl or -[C(R) 2 ] P -R 6 ; wherein p is 0-6; or any two occurrences of R 5 can be taken together to form a 4-8 membered optionally substituted ring which contains 0-3 heteroatoms selected from N, O, S, and P; each R 6 is independently hydroxyl, -N(R)COR, -N(R)C(O)OR, -N(R)SO 2 (R), -C(O)N(R) 2 , -OC(O)N(R)(R), -SO 2 N(R)(R), -N(R)(R), -COOR, -C(O)N(OH)(R), -OS(O) 2 OR, -C(O)N(OH)(
  • R 1 is H, hydroxyl, alkoxyl, aryloxy, or amino.
  • R 3 is H and/or R 4 is H, alkyl, hydroxyl, aralkyl, -[C(R) 2 ] q -R 5 , -[(W)-N(R)C(0)] q R 5 , -[(W)-N(R)SO 2 ] q R 5 , -[(W)-C(0)N(R)] q R 5 , -[(W)-0] q R 5 , -[(W)-C(0)] q R 5 , or -[(W)-C(0)0] q R 5 .
  • R 1 is H or -OR
  • R 2 is H or alkyl
  • R 4 is H.
  • R 2 is H or alkyl
  • R 3 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, or aralkyl
  • R 4 is H, alkyl, aralkyl, -[(W)-N(R)C(0)] q R 5 , -[(W)-N(R)SO 2 ] q R 5 , -[(W)-C(0)N(R)] q R 5 , -[(W)-0] q R 5 , -[(W)-C(0)] q R 5 , or -[(W)-C(0)0] q R 5 .
  • R 1 is sulfonamide
  • the present invention relates to a compound selected from the group consisting of:
  • the compounds mentioned above are isolated.
  • the present invention relates to an isolated compound selected from the group consisting of:
  • the present invention relates to a compound represented by the following structure: or a pharmaceutically acceptable salt thereof; wherein R 1 is H, alkyl, -OR, amino, sulfonamido, sulfamido, -OC(O)R 5 , - N(R 5 )C(O)R 5 , or a sugar;
  • R 3 is H, alkyl, alkenyl, or alkynyl
  • R 4 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR 5 , -C(O)R 5 , -CO 2 R 5 , -SO 2 R 5 , -C(O)N(R 5 )(R 5 ), -[C(R) 2 ] q -R 5 , -[(W)-N(R)C(0)] q R 5 , -[(W)-C(0)] q R 5 , -[(W)-C(0)0] q R 5 , -[(W)-0C(0)] q R 5 , -[(W)-SO 2 ] q R 5 , -[(W)-N(R 5 )SO 2 ] q R 5 , -[(W)-C(O)N(R 5
  • X " is a halide; each R is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl or -[C(R) 2 ] P -R 6 ; wherein p is 0-6; or any two occurrences of R 5 can be taken together to form a 4-8 membered optionally substituted ring which contains 0-3 heteroatoms selected from N, O, S, and P; each R 6 is, independently, hydroxyl, -N(R)COR, -N(R)C(O)OR, -N(R)SO 2 (R), -C(O)N(R) 2 , -OC(O)N(R)(R), -SO 2 N(R)(R), -N(R)(R), -COOR, -C(O)N(OH)(R), -OS(O) 2
  • R 8 and R 9 are H;
  • the compound is epimerically pure and/or isolated.
  • R 4 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR 5 , -[C(R) 2 ] q -R 5 , -[(W)-N(R)C(0)] q R 5 , -[(W)-C(0)] q R 5 , -[(W)-C(0)0] q R 5 , -[(W)-0C(0)] q R 5 , -[(W)-SO 2 ] q R 5 , -[(W)-N(R 5 )SO 2 ] q R 5 , -[(W)-C(O)N(R 5 )] q R 5 , -[(W)-0] q R
  • the present invention relates to a compound selected from the group consisting of:
  • the above compounds are epimerically pure and/or isolated.
  • the present invention relates to an epimerically pure compound selected from the group consisting of:
  • Another aspect of the present invention relates to a pharmaceutical composition including any of the aforementioned compounds, and a pharmaceutically acceptable excipient.
  • the present invention relates to a process for preparing cyclopropyl derivatives of cyclopamine and related analogs having the formula 136:
  • Y is CR 7 R 8 ;
  • R 1 is H, alkyl, amino, hydroxyl, carboxyl, carbamoyl, alkoxy, hydroxyl, sugar or a protected hydroxyl group;
  • R ' 3 , R " 4 , a aniidu R K. 5 i iss,, i unidueeppeeniidueeniitLliyy,, H n,, a alik ⁇ yyli,, a alik ⁇ eeniiyyli,, a alik ⁇ y; nyl, aryl, cycloalk kyyll,, hheetteerrooccyyccllooaallkkyyll,, aarralkyl, heteroaryl, or heteroaralkyl; or R 3 and R 4 or R 4 and R 31 taken together form a bond; R is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl,
  • the process includes the steps of contacting a compound of formula 136a with a haloalkylzinc phosphate cyclopropanating agent to yield a compound of formula 136:
  • R 1 , R 2 , R 3 , R 4 , R 5 , R 6 are as defined in compound 136.
  • the present invention provides methods for preparing a compound of formula 137:
  • Y is CR 7 R 8 ;
  • R 1 is H, alkyl, amino, hydroxyl, carboxyl, carbamoyl, alkoxy, hydroxyl, sugar or a protected hydroxyl group;
  • R is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR 9 , -C(O)R 9 , -CO 2 R 9 , -SO 2 R 9 , -C(O)N(R 9 )(R 9 ), -[C(R 9 ) 2 ] q R 9 , -[(W)-N(R 9 )C(O)] q R 9 , -[(W)-C(0)] q R 9 , -[(W)-C(0)0] q R 9 , -[(W)-0C(0)] q R 9 , -[(W)-SO 2 ] q R 9 , -[(W)-N(R 9 )SO 2 ] q R 9 , -[(W)-C(O)N(
  • R 1 , R 2 , R 3 , R 4 , R , R and Y are as defined in compound 137; and then contacting the compound of formula 137b with an acid to give a compound of formula 137.
  • R 7 and R 8 can both be H; in other embodiments R 1 can be a protected hydroxyl; and/or R 6 is a nitrogen protecting group.
  • the haloalkylzinc phosphate cyclopropanating agent is formed by combining a phosphoric acid of formula 141a, a dialkylzinc, and a dihaloalkylane of formula 141b:
  • m is, independently for each occurrence, 0, 1, 2, 3, or 4; n is, independently for each occurrence, 0,1, or 2; and each of R 12 , R 13 , R 14 , R 15 , R 16 , R 17 and R 18 is, independently, alkyl, aryl, aralkyl, or halide.
  • the present invention relates to a process for preparing a compound of formula 142:
  • the process includes the steps of contacting a compound of formula 142a with a cyclopropanating agent to form a compound formula 142b;
  • Y is CR R ; R is a protected hydroxyl group;
  • R 2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; each of R 3 , R 4 , and R 5 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
  • R 6 is a nitrogen protecting group;
  • each of R 7 and R 8 is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester;
  • each R 9 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl.
  • R and R can both be H; in other embodiments the protected hydroxyl group can be an ester or a carbonate; the nitrogen protecting can be a
  • R carbamate or an amide R and R can both be H and the nitrogen protecting can be a carbamate or an amide; R 2 and R 3 can be H and R 4 and R taken together can form a bond; and/or the cyclopropanating agent is generated from a dihaloalkane and a metal species (e.g., dialkyl zinc or a zinc copper couple).
  • a metal species e.g., dialkyl zinc or a zinc copper couple
  • the cyclopropanating agent is generated from a dihaloalkane species and a dialkyl zinc species, and a phosphoric acid species or a salt thereof.
  • the phosphoric acid species can have a structure of formula 151:
  • each of R 10 and R 11 is independently alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R 10 and R 11 taken together have the formula 151a, 151b, or 151c;
  • n independently for each occurrence is 0,1, or 2; each of R 12 , R 13 , R 14 , R 15 , R 16 , R 17 and R 18 is, independently, alkyl, aryl, aralkyl, or halide.
  • the acid is a Bronsted acid (e.g., acetic acid, trifluoromethanesulfonic acid, phosphoric acid, methanesulfonic acid or HCl).
  • the acid is a Lewis acid (e.g., BF 3 , zinc chloride, zinc methanesulfonate, or a zinc salt).
  • the present invention also relates to a process for preparing a compound of formula 156:
  • the process includes the steps of: contacting a compound of formula 156a with a cyclopropanating agent to form a compound formula 156b;
  • R 1 is an oxygen protecting group selected from the group consisting of formate, acetate, chloroacetate, dichloroacetate, trichloroacetate, pivaloate, benzoate, alkyl carbonate, alkenyl carbonate, aryl carbonates, aralkyl carbonate, 2,2,2-trichloroethyl carbonate, alkoxymethyl ether, aralkoxymethyl ether, alkylthiomethl ether, aralkylthio ether, arylthio ether, trialkylsilyl ether, alkylarylsilyl ether, benzyl ether, arylmethyl ether, allyl ether; and R 2 is a nitrogen protecting group selected from the group consisting of formyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, phenyl acetyl, benzoyl
  • n independently for each occurrence is 0,1, or 2; each of R 12 , R 13 , R 14 , R 15 , R 16 , R 17 and R 18 is, independently, alkyl, aryl, aralkyl, or halide.
  • the oxygen protecting group can be, in some embodiments, selected from alkyl carbonates, aralkyl carbonates (e.g., benzylcarbonate), benzoates, pivaloate, or formate.
  • the nitrogen protecting group can be selected from benzoyl, trichloroacetyl, trifluoroacetyl, formyl, alkyl carbamates, aralkyl carbamates (e.g., benzylcarbamate), aryl carbamates, diarylphosphinamides, dialkylphosphinamidates, or diarylphosphinamidates.
  • each expression e.g., alkyl, m, n, etc., when it occurs more than once in any structure, is intended to be independent of its definition elsewhere in the same structure.
  • acylamino refers to a moiety that may be represented by the general formula:
  • R50 wherein R50 and R54 independently represent a hydrogen, an alkyl, an alkenyl or -(CH 2 ) m -R61, where R61 represents an aryl, a cycloalkyl, a cycloalkenyl, a heterocycle or a polycycle; and m is zero or an integer in the range of 1 to 8.
  • alkenyl and alkynyl refer to unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double or triple bond respectively.
  • alkoxyl refers to an alkyl group, as defined above, having an oxygen radical attached thereto.
  • Representative alkoxyl groups include methoxy, ethoxy, propyloxy, tert-butoxy and the like.
  • alkyl refers to the radical of saturated aliphatic groups, including straight-chain alkyl groups, branched-chain alkyl groups, cycloalkyl (alicyclic) groups, alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups.
  • a straight chain or branched chain alkyl has 30 or fewer carbon atoms in its backbone (e.g., C1-C30 for straight chain, C3-C30 for branched chain), 20 or fewer.
  • certain cycloalkyls have from 3-10 carbon atoms in their ring structure, and others have 5, 6 or 7 carbons in the ring structure.
  • alkylthio refers to an alkyl group, as defined above, having a sulfur radical attached thereto.
  • the "alkylthio" moiety is represented by one of -S-alkyl, -S-alkenyl, -S-alkynyl, and -S-(CH 2 ) m -R61, wherein m and R61 are defined above.
  • Representative alkylthio groups include methylthio, ethyl thio, and the like.
  • amino is art recognized as an amino-substituted carbonyl and includes a moiety that may be represented by the general formula:
  • R50 and R51 each independently represent a hydrogen, an alkyl, an alkenyl, -(CH 2 ) m -R61, R61 represents an aryl, a cycloalkyl, a cycloalkenyl, a heterocycle or a polycycle; and m is zero or an integer in the range of 1 to 8, or R50 and R51, taken together with the N atom to which they are attached complete a heterocycle having from 4 to 8 atoms in the ring structure. Certain embodiments of the amide in the present invention will not include imides which may be unstable.
  • amine and “amino” are art-recognized and refer to both unsubstituted and substituted amines, e.g., a moiety that may be represented by the general formulas:
  • R50 and R51 each independently represent a hydrogen, an alkyl, an alkenyl, or -(CH 2 ) m -R61, where R61 is defined as above.
  • alkylamine includes an amine group, as defined above, having a substituted or unsubstituted alkyl attached thereto, i.e., at least one of R50 and R51 is an alkyl group.
  • aralkyl refers to an alkyl group substituted with an aryl group (e.g., an aromatic or heteroaromatic group).
  • aryl as used herein includes 5-, 6- and 7-membered single-ring aromatic groups that may include from zero to four heteroatoms, for example, benzene, anthracene, naphthalene, pyrene, pyrrole, furan, thiophene, imidazole, oxazole, thiazole, triazole, pyrazole, pyridine, pyrazine, pyridazine and pyrimidine, and the like.
  • aryl groups having heteroatoms in the ring structure may also be referred to as "aryl heterocycles" or “heteroaromatics.”
  • the aromatic ring may be substituted at one or more ring positions with such substituents as described above, for example, halogen, azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, sulfonamido, ketone, aldehyde, ester, heterocyclyl, aromatic or heteroaromatic moieties, -CF3, -CN, or the like.
  • aryl also includes polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings (the rings are "fused rings") wherein at least one of the rings is aromatic, e.g., the other cyclic rings may be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls.
  • Random acid refers to any substance that can act as a hydrogen ion (proton) donor.
  • carboxyl is defined to include esters, thiocarboxyl, aldehydes, ketones and the like and thus includes such moieties as may be represented by the general formulas:
  • X50 is a bond or represents an oxygen or a sulfur
  • each of R55 and R56 represents independently a hydrogen, an alkyl, an alkenyl, -(CH 2 ) m -R61, where m and R61 are defined above.
  • dirtyical refers to any of a series of divalent groups from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, and heteroaralkyl
  • alkyl heteroaralkyl diradical.
  • Typical examples include alkylenes of general structure (CH 2 ) ⁇ where X is 1-6, and corresponding alkenylene and alkynylene linkers having 2-6 carbon atoms and one or more double or triple bonds; cycloalkylene groups having 3-8 ring members; and aralkyl groups wherein one open valence is on the aryl ring and one is
  • haloalkyl refers to an alkyl group where anywhere from 1 to all hydgrogens have been replaced with a halide.
  • a "perhaloalkyl” is where all of the hydrogens have been replaced with a halide.
  • heteroatom as used herein means an atom of any element other than carbon or hydrogen.
  • heteroatoms include boron, nitrogen, oxygen, phosphorus, sulfur and selenium.
  • heterocyclyl or “heterocyclic group” refer to 3- to 10- membered ring structures, in some instances from 3- to 7-membered rings, whose ring structures include one to four heteroatoms. Heterocycles can also be polycycles.
  • Heterocyclyl groups include, for example, thiophene, thianthrene, furan, pyran, isobenzofuran, chromene, xanthene, phenoxathiin, pyrrole, imidazole, pyrazole, isothiazole, isoxazole, pyridine, pyrazine, pyrimidine, pyridazine, indolizine, isoindole, indole, indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine, naphthyridine, quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline, phenanthridine, acridine, pyrimidine, phenanthroline, phenazine, phenarsazine, phenothiazine, furazan, phenoxazine, pyrrolidine, o
  • the heterocyclic ring may be substituted at one or more positions with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, -CF3, -CN, or the like.
  • substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl,
  • isolated in connection with a compound of the present invention means the compound is not in a cell or organism and the compound is separated from some or all of the components that typically accompany it in nature.
  • Lower alkyl as used herein means an alkyl group, as defined above, but having from one to ten carbons, in some embodiments from one to six carbon atoms in its backbone structure. Likewise, “lower alkenyl” and “lower alkynyl” have similar chain lengths. Certain alkyl groups are lower alkyls. In some embodiments, a substituent designated herein as alkyl is a lower alkyl.
  • nitro means -NO2; the term “halogen” designates -F, -Cl, -Br or -I; the term “sulfhydryl” means -SH; the term “hydroxyl” means -OH; and the term “sulfonyl” means -SO2-.
  • polycyclyl or “polycyclic group” refer to two or more rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are "fused rings". Rings that are joined through non-adjacent atoms are termed "bridged" rings.
  • Each of the rings of the polycycle may be substituted with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, -CF3, -CN, or the like.
  • substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl
  • epimerically pure in connection with a compound of the present invention means that the compound is substantially free of stereoisomers of the compound wherein the configuration of the stereogenic center that R 3 is bonded to is inverted.
  • an epimerically pure compound represented by the following formula:
  • R 1 , R 2 , R 3 , R 4 , R 7 , R 7 , R 8 , and R 9 are as defined below, is substantially free of compounds represented by the following formula:
  • R 1 , R 2 , R 3 , R 4 , R 7 , R 7 , R 8 , and R 9 are as defined below.
  • Epimerically pure compounds contain less than about 20 % by mass, less than about 15% by mass, less than about 10% by mass, less than about 5% by mass, or less than about 3% by mass of stereoisomeric compounds wherein the configuration of the stereogenic center that R 3 is bonded to is inverted relative to the compound.
  • protecting group means temporary substituents which protect a potentially reactive functional group from undesired chemical transformations.
  • protecting groups include esters of carboxylic acids, silyl ethers of alcohols, and acetals and ketals of aldehydes and ketones, respectively.
  • the field of protecting group chemistry has been reviewed (Greene, T. W.; Wuts, P.G.M. Protective Groups in Organic Synthesis, 2 nd ed.; Wiley: New York, 1991).
  • the functional group being protected and the protecting group are together referred to as one moiety.
  • the fragment shown below is sometimes referred to as a benzyl carbonate; i.e., the protected (underlined) O makes up part of the carbonate.
  • saccharide refers to a natural or an unnatural monosaccharide, disaccharide or oligosaccharide comprising one or more pyranose or furanose rings.
  • the sugar may be covalently bonded to the steroidal alkaloid of the present invention through an ether linkage or through an alkyl linkage.
  • the saccharide moiety may be covalently bonded to a steroidal alkaloid of the present invention at an anomeric center of a saccharide ring.
  • Sugars may include, but are not limited to ribose, arabinose, xylose, lyxose, allose, altrose, glucose, mannose, gulose, idose, galactose, talose, glucose, and trehalose.
  • R50 O O wherein R50 and R56 are as defined above.
  • triflyl refers to trifluoromethanesulfonyl, p-toluenesulfonyl, methanesulfonyl, and nonafluorobutanesulfonyl groups, respectively.
  • triflate refers to trifluoromethanesulfonate ester, p-toluenesulfonate ester, methanesulfonate ester, and nonafluorobutanesulfonate ester functional groups and molecules that contain the groups, respectively.
  • substitution or “substituted with” includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc.
  • Certain compounds of the present invention may exist in particular geometric or stereoisomeric forms.
  • the present invention contemplates all such compounds, including CM- and trans -isomers, R- and 5-enantiomers, diastereomers, (D)- isomers, (L)-isomers, the racemic mixtures thereof, and other mixtures thereof, as falling within the scope of the invention.
  • Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in this invention.
  • certain embodiments of the present compounds may contain a basic functional group, such as amino or alkylamino, and are, thus, capable of forming pharmaceutically-acceptable salts with pharmaceutically-acceptable acids.
  • pharmaceutically-acceptable salts refers to the relatively non-toxic, inorganic and organic acid addition salts of compounds of the present invention. These salts can be prepared in situ in the administration vehicle or the dosage form manufacturing process, or by separately reacting a purified compound of the invention in its free base form with a suitable organic or inorganic acid, and isolating the salt thus formed during subsequent purification.
  • Representative salts include the hydrobromide, hydrochloride, sulfate, bisulfate, phosphate, nitrate, acetate, valerate, oleate, palmitate, stearate, laurate, benzoate, lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate, tartrate, napthylate, mesylate, glucoheptonate, lactobionate, and laurylsulphonate salts and the like.
  • sulfate bisulfate
  • phosphate nitrate
  • acetate valerate
  • oleate palmitate
  • stearate laurate
  • benzoate lactate
  • phosphate tosylate
  • citrate maleate
  • fumarate succinate
  • tartrate napthylate
  • mesylate mesylate
  • glucoheptonate lactobionate
  • laurylsulphonate salts and the like See, for example, Berg
  • the pharmaceutically acceptable salts of the compounds of the present invention include the conventional nontoxic salts or quaternary ammonium salts of the compounds, e.g., from non-toxic organic or inorganic acids.
  • such conventional nontoxic salts include those derived from inorganic acids such as hydrochloride, hydrobromic, sulfuric, sulfamic, phosphoric, nitric, and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, palmitic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicyclic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isothionic, and the like.
  • the compounds of the present invention may contain one or more acidic functional groups and, thus, are capable of forming pharmaceutically- acceptable salts with pharmaceutically-acceptable bases.
  • pharmaceutically- acceptable salts refers to the relatively non-toxic, inorganic and organic base addition salts of compounds of the present invention. These salts can likewise be prepared in situ in the administration vehicle or the dosage form manufacturing process, or by separately reacting the purified compound in its free acid form with a suitable base, such as the hydroxide, carbonate or bicarbonate of a pharmaceutically-acceptable metal cation, with ammonia, or with a pharmaceutically- acceptable organic primary, secondary or tertiary amine.
  • Representative alkali or alkaline earth salts include the lithium, sodium, potassium, calcium, magnesium, and aluminum salts and the like.
  • Representative organic amines useful for the formation of base addition salts include ethylamine, diethylamine, ethylenediamine, ethanolamine, diethanolamine, piperazine and the like. (See, for example, Berge et al, supra)
  • the ring expanded steroidal alkaloid derivatives described above can be prepared directly from naturally occurring steroidal alkaloids or synthetic analogs thereof.
  • the steroidal alkaloid starting materials can be cyclopamine or jervine. These steroidal alkaloids can be purchased commercially or extracted from Veratrum Californicum.
  • the process of the present invention comprises the steps of cyclopropanating suitable starting steroidal alkaloid derivatives followed by ring expansion rearrangement of the cyclopropyl derivatives. In some instances, it may be desirable to suitably protect or otherwise transform reactive functionalities present on the molecule prior to cyclopropanation.
  • an alcohol present at R 1 and a secondary nitrogen present on the fused furano-piperidine ring can both be protected prior to cyclopropanation.
  • protecting groups that are efficiently added and removed from the alkaloid, yield intermediates in the synthetic process with improved handling properties and which allow for the efficient purification of the synthetic intermediates formed may be preferred.
  • oxygen protecting groups include, but are not limited to formate, acetate, chloroacetate, dichloroacetate, trichloroacetate, pivaloate, benzoates, alkyl carbonate, alkenyl carbonate, aryl carbonates, aralkyl carbonate (e.g., benzyl carbonate), 2,2,2-trichloroethyl carbonate, alkoxymethyl ether, aralkoxymethyl ether, alkylthiomethl ether, aralkylthio ether, arylthio ether, trialkylsilyl ether, alkylarylsilyl ether, benzyl ether, arylmethyl ether, and allyl ether.
  • formate acetate, chloroacetate, dichloroacetate, trichloroacetate, pivaloate
  • benzoates alkyl carbonate, alkenyl carbonate, aryl carbonates, aralkyl carbonate (e.g., benzyl
  • nitrogen protecting groups include, but are not limited to formyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, phenyl acetyl, benzoyls, benzamides, alkyl carbamates, aralkyl carbamates (e.g., benzyl carbamates), aryl carbamates, allyl, aralkyl, alkoxymethyl, aralkoxymethyl, N-2-cyanoethyl, diary lphosphinamides, dialkylphosphinamidates, diarylphosphinamidates, and trialkylsilyl.
  • cyclopropanating agents can be used to cyclopropanate the steroidal alkaloid.
  • 1 -haloalkylmetal complexes and reactive species referred to as carbenoids are commonly used to cyclopropanate olefins.
  • These reagents are typically made using a diiodoalkane or diazoalkane and a metal or organometalic species such as Et 2 Zn, JBu 3 Al, samarium, copper, rhodium, or palladium.
  • Et 2 Zn and diiodomethane are used to generate the 1,1 -haloalkylmetal species.
  • the reactivity and the ease of handling of the 1,1 -haloalkylzinc complexes can be modified by the addition of certain reagents, such as acids. It is believed that the addition of an acid to the 1,1 -haloalkylzinc species generates an alkyl zinc mixed salt.
  • a biarylphosphoric acid is combined with diiodomethane and diethylzinc to generate a putative haloalkyl zinc phosphate cyclopropanating agent.
  • a variety of phosphoric acids can be used to generate the putative haloalkylzinc phosphate.
  • cyclopropanation methods such as those utilizing sulfur ylides to react with an olefin conjugated to a carbonyl to add a CH 2 or CH-alkyl or CH- aryl group, and metal-catalyzed decomposition of diazoalkyl and ⁇ -diazo-carbonyl compounds, such as diazomethane and ethyl diazoacetate, can also be used: these methods readily provide cyclopropanes having alkyl, aryl, alkoxycarbonyl (-COOR), or acyl substituents. Additional cyclopropanating agents are described in Masalov et al., Organic Letters (2004) Vol. 6, pp. 2365-8 and Hansen et al., Chem. Comm. (2006) 4838- 40.
  • the cyclopropyl ring may be substituted or unsubstituted. In cases where the cyclopropyl ring is substituted, the groups attached to the methylene of the cyclopropane will be installed onto the D ring after rearrangement and ring expansion. [0073] The cyclopropanation reactions may be conducted in an aprotic solvent.
  • Suitable solvents include ethers, such as diethyl ether, 1,2-dimethoxyethane, diglyme, t- butyl methyl ether, tetrahydrofuran and the like; halogenated solvents, such as chloroform, dichlorome thane, dichloroethane, and the like; aliphatic or aromatic hydrocarbon solvents, such as benzene, xylene, toluene, hexane, pentane and the like; esters and ketones, such as ethyl acetate, acetone, and 2-butanone; polar aprotic solvents, such as acetonitrile, dimethylsulfoxide, dimethylformamide, and the like; or combinations of two or more solvents.
  • dichlorome thane is the solvent used for the cyclopropanation when a dialkyl zinc and diiodomethane is used.
  • a solution containing the cyclopropanating agent is prepared by first adding a solution of a phosphoric acid to a solution of diethylzinc, followed by addition of diiodomethane to the reaction solution.
  • the cyclopropanation substrate is then added to this solution.
  • the cyclopropanation agent can be prepared in the presence of the cyclopropanation substrate by changing the order of addition of the reagents.
  • the cyclopropanation reaction is conducted by first adding the phosphoric acid to a solution of dialkylzinc, followed by the addition of the cyclopropanation substrate, and finally the dihaloalkane is added.
  • cyclopropanating agent is generated under controlled conditions and immediately reacts with the cyclopropanation substrate.
  • the cyclopropanation methods described herein can also be used to cyclopropanate other polycyclic compounds, for example, those with steroidal backbones.
  • the compound may be derivatized using a variety of functionalization reactions known in the art.
  • Representative examples include palladium coupling reactions to alkenylhalides or aryl halides, oxidations, reductions, reactions with nucleophiles, reactions with electrophiles, pericyclic reactions, radical reactions, installation of protecting groups, removal of protecting groups, and the like.
  • the cyclopropyl analogs undergo a rearrangement and ring expansion to afford steroidal alkaloid analogs in which the D ring has been expanded by one carbon.
  • the cyclopropanation and ring expansion can take place in a two-step one reaction vessel process or in a two-step two reaction vessel process.
  • the acid used to initiate the ring expansion rearrangement is added after completion of the cyclopropanation reaction.
  • the zinc salts that are generated in the course of cyclopropanating the steroidal alkaloid can themselves act as Lewis acids to catalyze the ring expansion rearrangement.
  • the reactivity of the zinc salts generated after the cyclopropanation can be modified by the addition of acids to generate more active Lewis acids.
  • the methanesulfonic acid is added to the cyclopropanation reaction vessel after completion of the cyclopropanation.
  • suitable acids include, but are not limited to zinc salts, boron compounds, magnesium salts, titanium salts, indium salts, aluminum salts, tin salts, lanthanum salts, trifluoromethanesulfonic acid, diaryloxyphosporic acids, acetic acid, and HCl.
  • the Lewis acid used is a zinc salt or BF 3 .
  • ring expanded analogs may be further functionalized using a variety of functionalization reactions known in the art.
  • Representative examples include palladium coupling reactions to alkenylhalides or aryl halides, oxidations, reductions, reactions with nucleophiles, reactions with electrophiles, pericyclic reactions, radical reactions, installation of protecting groups, removal of protecting groups, and the like.
  • Hedgehog signaling is essential in many stages of development, especially in formation of left-right symmetry. Loss or reduction of hedgehog signaling leads to multiple developmental deficits and malformations, one of the most striking of which is cyclopia.
  • lung cancer (Watkins et al. (2003) Nature 422: 313-317), prostate cancer (Karhadkar et al (2004) Nature 431 : 707-12, Sheng et al. (2004) Molecular Cancer 3: 29-42, Fan et al. (2004) Endocrinology 145: 3961-70), breast cancer (Kubo et al. (2004) Cancer Research 64: 6071-74, Lewis et al. (2004) Journal of Mammary Gland Biology and Neoplasia 2: 165-181) and hepatocellular cancer (Sictician et al. (2005) ASCO conference, Mohini et al. (2005) AACR conference).
  • small molecule inhibition of the hedgehog pathway has been shown to inhibit the growth of basal cell carcinoma (Williams, et al., 2003 PNAS 100: 4616-21), medulloblastoma (Berman et al., 2002 Science 297: 1559-61), pancreatic cancer (Berman et al., 2003 Nature 425: 846-51), gastrointestinal cancers (Berman et al., 2003 Nature 425: 846-51, published PCT application WO 05/013800), esophageal cancer (Berman et al., 2003 Nature 425: 846-51), lung cancer (Watkins et al., 2003. Nature 422: 313-7), and prostate cancer (Karhadkar et al., 2004. Nature 43J_: 707-12).
  • the present invention provides pharmaceutically acceptable compositions which comprise a therapeutically-effective amount of one or more of the compounds described above, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents.
  • the pharmaceutical compositions of the present invention may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, capsules, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin; (4) intravaginally or intrarectally, for
  • aqueous and nonaqueous carriers examples include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate.
  • polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
  • vegetable oils such as olive oil
  • injectable organic esters such as ethyl oleate.
  • Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
  • compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents, dispersing agents, lubricants, and/or antioxidants.
  • adjuvants such as preservatives, wetting agents, emulsifying agents, dispersing agents, lubricants, and/or antioxidants.
  • Prevention of the action of microorganisms upon the compounds of the present invention may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like.
  • isotonic agents such as sugars, sodium chloride, and the like into the compositions.
  • prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as aluminum monostearate and gelatin.
  • Methods of preparing these formulations or compositions include the step of bringing into association a compound of the present invention with the carrier and, optionally, one or more accessory ingredients.
  • the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.
  • the compounds of the present invention are administered as pharmaceuticals, to humans and animals, they can be given per se or as a pharmaceutical composition containing, for example, about 0.1 to 99%, or about 10 to 50%, or about 10 to 40%, or about 10 to 30, or about 10 to 20%, or about 10 to 15% of active ingredient in combination with a pharmaceutically acceptable carrier.
  • compositions of the present invention may be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.
  • the selected dosage level will depend upon a variety of factors including the activity of the particular compound of the present invention employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion or metabolism of the particular compound being employed, the rate and extent of absorption, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compound employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.
  • a suitable daily dose of a compound of the invention will be that amount of the compound which is the lowest dose effective to produce a therapeutic effect. Such an effective dose will generally depend upon the factors described above.
  • oral, intravenous and subcutaneous doses of the compounds of the present invention for a patient when used for the indicated effects, will range from about 0.0001 to about 100 mg, or about 0.001 to about 100 mg, or about 0.01 to about 100 mg, or about 0.1 to about 100 mg per, or about 1 to about 50 mg per kilogram of body weight per day.
  • the subject receiving this treatment is any animal in need, including primates, in particular humans, and other mammals such as equines, cattle, swine and sheep; and poultry and pets in general.
  • Recrystallized cyclopamine 2 (14.1 g, 34.0 mmol, 1 eq) is dissolved in anhydrous DCM (70 mL) and anhydrous MeOH (29 mL). The clear solution is cooled, and triethylamine (10.4 g, 102.7 mmol, 3 eq) followed by benzyl chloroformate (6.20 g, 36.3 mmol, 1.1 eq) is added. After the addition is complete, the solution is stirred in the ice bath for 30 mm. Three portions of benzyl chloroformate (3 X 0.35 g, 3.46 mmol, 0.03 eq) are added over the 3 h.
  • the reaction is slowly quenched with water (71 mL), while maintaining the temperature below 20 0 C.
  • the mixture is stirred for 15 mm before the layers are settled and separated.
  • the organic layer is dried over sodium sulfate and filtered.
  • the combined filtrate is buffered with anhydrous pyridine (30 mL), concentrated, and solvent exchanged with additional anhydrous pyridine (43 mL) and concentrated.
  • Bis(2,6-dimethyphenyl)phosphate (10.65 g, 34.8 mmol, 3.1 eq) is dried by concentration from anhydrous DCM (42 mL) and held under a nitrogen atmosphere. The phosphate is then redissolved in anhydrous DCM (110 mL). In a separate flask, a solution of neat diethylzinc (4.17 g, 33.8 mmol, 3.0 eq) in anhydrous DCM (35 mL) is prepared and cooled to -25 0 C. The phosphate solution is slowly transferred to the vessel containing the diethylzinc solution over 1 h, maintaining the temperature at or below -10 0 C.
  • the solution is filtered under nitrogen, and the filtrate is washed with a 2 % (wt/wt) aqueous solution of ethylenediamine (125 mL) then water (130 mL), and then dried over sodium sulfate.
  • the drying agent is removed by filtration and the filtrate is concentrated to dryness under vacuum.
  • the solids that remained are chased with toluene (2 x 55 mL) on the rotary evaporator and the resulting material used without further purification in the next step
  • a round bottom flask is sequentially charged with the homo-allylic alcohol (7.50 g, 17.6 mmol, 1 eq), aluminum tri-fe?t-butoxide (6.10 g, 24.8 mmol, 1.4 eq), anhydrous toluene ( 115 mL), and 2-butanone (90 g, 1.24 mol, 7 eq).
  • the suspension is heated under a nitrogen atmosphere to 75 0 C for 16 h.
  • the reaction temperature is then allowed to cool to 49 0 C.
  • Aqueous 20 % (w/w) potassium sodium tartrate solution (226 g) is added to the stirred suspension.
  • the suspension is stirred at rt for 3.5 h.
  • the layers are separated.
  • Cyclopamine 2 (5.02 g, 12.2 mmol, 1.0 eq) is dissolved in anhydrous pyridine (25 mL).
  • DMAP 300 mg, 2.44 mmol, 0.2 eq.
  • triethyl amine 5.5 mL, 39.1 mmol, 3.2 eq
  • BtO-Cbz 10.5 g, 39.1 mmol, 3.2 eq
  • the mixture is cooled to rt, treated with 30 mL water, heated to get a homogeneous solution and allowed to cool to room temp.
  • a round bottom flask is sequentially charged with the homo-allylic alcohol 8 (7.50 g, 17.6 mmol, 1 eq), aluminum tri-fe?t-butoxide (6.10 g, 24.8 mmol, 1.4 eq), anhydrous toluene (115 mL), and 2-butanone (90 g, 1.24 mol, 7 eq).
  • the suspension is heated under a nitrogen atmosphere to 75 0 C for 16 h.
  • the reaction temperature is then allowed to cool to 49 0 C.
  • Aqueous 20 % (w/w) potassium sodium tartrate solution (226 g) is added to the stirred suspension.
  • the suspension is stirred at rt for 3.5 h.
  • the layers are separated.
  • ketone 6 85 mg, 0.199 mmol, 1 equiv. was charged and triethyleneglycol (2 mL) was added followed by hydrazine monohydrate (500 mg, 10 mmol, 50 equiv.) and potassium carbonate (138 mg, 1 mmol, 5 equiv.).
  • the tube was sealed and the reaction was heated at 150 0 C for 16 h.
  • the reaction was cooled to rt and water was added.
  • the residue was extracted with chloroform (3X).
  • the combined organic layers are washed with water, dried over Na 2 SO 4 , and concentrated to dryness.
  • the colorless oil was purified using silica gel flash chromatography (DCM/MeOH 96:4).
  • the reaction was cooled to rt and water was added.
  • the residue was extracted with MTBE (3X).
  • the organic layers were combined washed with brine, dried over Na 2 SO 4 , filtered, and concentrated to dryness.
  • the white foam was purified using silica gel flash chromatography (DCM/MeOH 99:1) to give 206 mg of the N-isopropyl derivative as a white foam.
  • the crude was purified using silica gel flash chromatography (hexane/EtOAc (9:1 to 4: 1)) to give the N-O derivative product (60 mg, 0.11 mmol) as a white foam.
  • This foam was dissolved in 2 mL of MeOH followed by 2N aqueous KOH (0.4 mL). The reaction mixture was stirred for Ih. Most of the MeOH was evaporated under a stream of nitrogen and IN HCl (500 ⁇ L) was added. The material was extracted with DCM (3X). The combined organic layers were washed with water, dried over Na 2 SO 4 , filtered and concentrated under reduced pressure.
  • Recrystallized cyclopamine (2.07 g) is charged to an appropriately sized reaction vessel and placed under an inert atmosphere.
  • EtOAc (7.6 g), triethylamine (1.53 g), and DMAP (307 mg) are added sequentially.
  • the suspension is warmed to 4O 0 C.
  • Cbz-OBt is added in three portions over 90 minutes, keeping the internal temperature below 45 0 C.
  • the reaction mixture is stirred at 4O 0 C for 90 minutes.
  • the temperature is maintained while methanol (26.4 g) is slowly added to the reaction mixture.
  • the resulting suspension is cooled to room temperature and stirred for at least 15 hours.
  • the crude product is collected by filtration and rinsed with methanol (5 g).
  • the white solid is dried under vacuum to a constant weight and recrystallized from heptane (30.3 g) and toluene (3.2 g) to afford Compound 24a (3.0 g).
  • Johnson Matthey Pd/C catalyst A-305038-5 (890 mg) is charged to an appropriately sized reaction vessel, followed by 24b (2.24 g).
  • the reaction vessel is purged with N 2 and toluene (21.8 g) and 2-propanol (6.7 g) are added sequentially.
  • the system is degassed and placed under a nitrogen atmosphere, and the process is repeated with hydrogen.
  • the system is stirred vigorously and the hydrogen blanket is maintained at one atmosphere for 4-5 hours.
  • the reaction is monitor by either TLC or HPLC. If incomplete, the reaction is inerted, additional catalyst (145 mg) is charged, and the hydrogen atmosphere is returned for another hour. Ethylenediamine (12.9 mg) is charged and the mixture was stirred for 15 minutes.
  • the catalyst is removed by filtration with a toluene:IPA (3:1) rinse.
  • the filtrate and rinses are concentrated and solvent exchanged to toluene.
  • the product is crystallized from toluene (19.0 g) and heptane (18.0 g) to afford 24c as a white crystalline solid (1.34 g, 98% yield).
  • 24c (644 mg) is charged to an appropriately sized reaction vessel followed by aluminum t-butoxide (525 mg), toluene (8.34 g, 15 vol), and 2-butanone (7.83 g, 15 vol).
  • the contents of the flask are degassed with evacuation/nitrogen purge cycles to remove oxygen and the reaction mixture is heated at 75°C with vigorous stirring for 16-18 hours.
  • the reaction is quenched by the addition of aqueous Rochelle's salt (2.6 g in 10.3 g water) and the mixture vigorously stirred for one hour at 45 0 C.
  • the aqueous and organic layers are separated.
  • the aqueous layer is back extracted with a mixture of toluene (2.9 g) and EtOAc (2.9 g).
  • the enone 24d (459 mg) and Johnson-Matthey 5% palladium on carbon (A503023-5, 101 mg) are charged to an appropriately sized multi neck reaction vessel.
  • the vessel is purged with nitrogen and 3-picoline (2.2 g) is charged as the solvent. Stirring is started and the vessel is first degassed using nitrogen and then stirred under hydrogen at atmospheric pressure for 8 hours.
  • the catalyst is removed by filtration through 0.2 micron media, rinsing with ACN (1.4 ml). The filtrate and rinse are combined in a clean reaction vessel equipped with mechanical stirring, an internal temperature probe, and a nitrogen atmosphere.
  • citric acid (3.7 g) in water (9.2 ml) is charged to the reaction vessel at or below 3O 0 C, and IPI-335589 is allowed to slowly crystallize from solution as the citrate salt at 20 and then O 0 C.
  • the crystalline product is recovered by suction filtration and washed with water (3.7 ml). After drying, the citrate salt, 24e, is isolated as a hydrate (3-5 wt% water) in 89.5% yield (622 mg) with a ⁇ : ⁇ ratio approaching 90:1.
  • the reaction is quenched at low temperature with MeOH (0.33 g), then 3M NaOH (2.4 g) at -20 0 C and 15% hydrogen peroxide in water (1.04 g) at or below 5°C, then stirring overnight at ambient temperatures.
  • the layers are split and the organic layer is washed sequentially with IM aqueous NaOH (2 ml), 0.5 M aqueous Na 2 SO 3 (2 ml), and water (2 ml) adjusted to a pH of 3 with HCl.
  • the organic layer is dried over sodium sulfate (0.82 g), filtered and concentrated.
  • the product 24g (0.457 g) is re-concentrated from DCM (0.9 g) and used in the next reaction.
  • the layers are separated and the organic layer is washed with 2.5 wt% sodium bicarbonate (13.8 g) and then water (10.9 g). The organic layer is dried over of sodium sulfate (4 g), filtered, and concentrated.
  • the product solution is solvent exchanged via charge and concentration to t-butyl methyl ether (10.9 ml) and then l,3-dimethyl-3,4,5,6-tetrahydro- 2(lH)-pyrimidinone (DMPU, 4.7 ml). The DMPU solution is used directly in the next reaction.
  • 24j (1.09 g) is dissolved and transferred to an appropriately sized reaction vessel with anhydrous DCM (15.8 g) and placed under a nitrogen atmosphere. The solution is cooled to 0 0 C. N,N-diisopropylethylamine (357 mg) and neat methanesulfonyl chloride (0.165 ml) are charged sequentially while maintaining temperature between below 5 0 C. The reaction is monitored by HPLC. Incomplete reactions are driven to completion with additional methanesulfonyl chloride. The reaction is quenched with 0.4 M aqueous sodium bicarbonate (11.4 g) and warmed to ambient temperature. The layers are separated and the aqueous phase is back extracted with DCM (5.8 g). The combined organic layers are dried over magnesium sulfate (0.55 g), filtered and concentrated. The product 24k is dissolved and striped from 2- propanol (4.0 g) to remove residual DCM and used directly in the next reaction.
  • the reaction is stirred under 1 atm of hydrogen for another 15 hours at ambient temperature.
  • the reaction is monitored by HPLC. Incomplete reactions are treated with additional catalyst and hydrogen.
  • the reaction is filtered, treated with steam activated carbon (200 mg), and filtered again.
  • the solution is dried by partial concentration transferred to a reaction vessel and diluted with anhydrous 2-propanol to 0.09 M based on the theoretical yield.
  • a 1.25 M HCl solution in 2- propanol (1.64 g) is charged over 20 minutes.
  • the hydrochloride salt crystallizes slowly with gentle stirring and is isolated by filtration.
  • the crystals are washed with 2-propanol (2.5 g) and vacuum dried to afford Compound 42 (916 mg, 80% yield) as a 1:1 IPA solvate.
  • Step B The mixture was diluted with CH 2 CI 2 (30 mL) and washed with three portions (30 mL each) of water. The organic layer was dried over Na 2 SO 4 , filtered, and evaporated to dryness. The desired white solid 51 was taken to the next step without purification.
  • the ketone 57 was azeotroped a couple times with CH 2 CI 2 and dried under vacuum for 1 h. Under nitrogen, the ketone 2 (693 mg, 1.27 mmol, 1 equiv.) was dissolved in anhydrous THF (20 mL) and the solution was cooled to -78C. A I M solution of K-selectride in THF (1.9 mL, 1.9 mmol, 1.5 equiv.) was added dropwise. After 1 h, the reaction was complete by TLC. The reaction was quenched by addition of 2.6 mL of 5 N NaOH followed by slow addition of 2.6 mL of 30% wt H 2 O 2 .
  • Example 28 Inhibition of the Hedgehog pathway in cell culture
  • Hedgehog pathway specific cancer cell killing effects may be ascertained using the following assay.
  • C3H10T1/2 cells differentiate into osteoblasts when contacted with the sonic hedgehog peptide (Shh-N). Upon differentiation; these osteoblasts produce high levels of alkaline phosphatase (AP) which can be measured in an enzymatic assay (Nakamura et al., 1997 BBRC 237: 465).
  • AP alkaline phosphatase
  • Compounds that block the differentiation of C3H10T1/2 into osteoblasts can therefore be identified by a reduction in AP production (van der Horst et al., 2003 Bone 33: 899).
  • the assay details are described below.
  • the results approximate (EC 50 for inhibition) of the differentiation assay is shown below in Table 1.
  • Mouse embryonic mesoderm fibroblasts C3H10T1/2 cells obtained from ATCC were cultured in Basal MEM Media (Gibco/Invitrogen) supplemented with 10% heat inactivated FBS (Hyclone), 50 units/ml penicillin and 50ug/ml streptomycin (Gibco/Invitrogen) at 37C with 5% CO2 in air atmosphere.
  • C3H10T1/2 cells were plated in 96 wells with a density of 8xlO 3 cells/well. Cells were grown to confluence (72hrs). After sonic Hedgehog (250ng/ml), and/or compound treatment, the cells were lysed in 110 ⁇ L of lysis buffer (50 mM Tris pH 7.4, 0.1% TritonXlOO), plates were sonicated and lysates spun through 0.2 ⁇ m PVDF plates (Corning). 40 ⁇ L of lysates was assayed for AP activity in alkaline buffer solution (Sigma) containing lmg/ml p-Nitrophenyl Phosphate.
  • lysis buffer 50 mM Tris pH 7.4, 0.1% TritonXlOO
  • the activity of Compound 42 was also evaluated in a transgenic mouse model of medulloblastoma. Mice that are heterozygous for loss of function mutations in the tumor suppressors Patchedl (Ptchl) and Hypermethylated in Cancer (Hicl) develop spontaneous medulloblastoma. Similar to human medulloblastoma, these tumors demonstrate complete promoter hypermethylation of the remaining Hicl allele, as well as loss of expression of the wild type Ptchl allele. When passaged as subcutaneous allografts, these tumors grow aggressively and are Hedgehog pathway-dependent. This model was employed to evaluate the efficacy of orally administered Compound, and to correlate activity with drug exposure in plasma and tumors. Oral administration (PO) of a single dose of Compound 42 led to dose-dependent down-regulation of the HH pathway in subcutaneously implanted tumors, as measured by decreased GIi-I mRNA expression 8 hours post dose administration.
  • Ptchl tumor suppressors Patchedl
  • LX22 cells were implanted subcutaneously into the flank of the right leg.
  • LX22 is primary xenograft model of SCLC derived from chemo -naive patients, which has been maintained by mouse to mouse passaging. This tumor responds to etoposide/carboplatin chemotherapy in way that closely resembles a clinical setting. LX22 regresses during chemotherapy treatment, goes through a period of remission, and then begins to recur.
  • Compound single agent activity and its ability to modulate the chemoresistant recurrence was tested.
  • mice were randomized into three dosing groups to receive Vehicle (30% HBPCD), Compound, or the chemotherapy combination of etoposide and carboplatin (E/P).
  • Compound 42 was administered at a dose of 40mg/kg/day, and after 16 consecutive doses there was no measurable difference between the treated and vehicle groups.
  • Etoposide was administered i.v at 12mg/kg on days 34, 35, 36, and 48, while Carboplatin was administered i.v. at 60mg/kg on days 34, 41, and 48, post tumor implant.
  • the E/P treated mice were further randomized to receive either Vehicle (30%HPBCD) or Compound follow up treatment.

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Abstract

The invention provides novel derivatives of cyclopamine having the following formula.

Description

CYCLOPAMINE ANALOGS
RELATED APPLICATIONS
[0001] This application claims priority to USSN 60/878,018, filed December 28, 2006, and USSN 60/941,596, filed June 1, 2007, both of which are hereby incorporated by reference in their entirety.
BACKGROUND OF THE INVENTION
[0002] The present invention generally relates to cyclopamine analogs and pharmaceutical compositions thereof, and methods for preparing such analogs and compositions. These compounds and compositions are useful for the treatment of disorders mediated by the hedgehog pathway, such as cancer.
[0003] Inhibition of the hedgehog pathway in certain cancers has been shown to result in inhibition of tumor growth. For example, anti-hedgehog antibodies have been shown to antagonize the function of the hedgehog pathway and inhibit the growth of tumors. Small molecule inhibition of hedgehog pathway activity has also been shown to result in cell death in a number of cancer types.
[0004] Research in this area has focused primarily on the elucidation of hedgehog pathway biology and the discovery of new hedgehog pathway inhibitors. Although inhibitors of the hedgehog pathway have been identified, there still exists the need to identify more potent inhibitors of the hedgehog pathway.
[0005] PCT publication WO 2006/026430 published 9 March 2006 and assigned to the same assignee as the present application, discloses a wide variety of cyclopamine analogs, focusing on those with unsaturation in the A or B ring. In the present application, the surprisingly potent analogs contain completely saturated A and B rings.
SUMMARY OF THE INVENTION
[0006] The present invention relates to analogs of steroidal alkaloids, such as cyclopamine, pharmaceutical compositions containing these compounds, and methods for preparing these compounds. In one embodiment, the present invention relates to a compound represented by the following structure:
Figure imgf000003_0001
or a pharmaceutically acceptable salt thereof; wherein R1 is H, alkyl, -OR, amino, sulfonamido, sulfamido, -OC(O)R5, - N(R5)C(O)R5, or a sugar;
R2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, nitrile, or heterocycloalkyl; or R1 and R2 taken together form =0, =S, =N(0R), =N(R), =N(NR2), =C(R)2;
R3 is H, alkyl, alkenyl, or alkynyl;
R4 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR5, -C(O)R5, -CO2R5, -SO2R5, -C(O)N(R5)(R5), -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-C(0)]qR5, -[(W)-C(0)0]qR5, -[(W)-0C(0)]qR5, -[(W)-SO2]qR5, -[(W)-N(R5)SO2]qR5, -[(W)-C(O)N(R5)]qR5, -[(W)-0]qR5, -[(W)-N(R)]qR5, -W-NR5S+X" or -[(W)-S]qR5; wherein each W is independently a diradical; each q is independently 1, 2, 3, 4, 5, or 6;
X" is a halide; each R5 is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl or -[C(R)2]P-R6; wherein p is 0-6; or any two occurrences of R5 can be taken together to form a 4-8 membered optionally substituted ring which contains 0-3 heteroatoms selected from N, O, S, and P; each R6 is independently hydroxyl, -N(R)COR, -N(R)C(O)OR, -N(R)SO2(R), -C(O)N(R)2, -OC(O)N(R)(R), -SO2N(R)(R), -N(R)(R), -COOR, -C(O)N(OH)(R), -OS(O)2OR, -S(O)2OR, -OP(O)(OR)(OR), -NP(O)(OR)(OR), or -P(O)(OR)(OR); and each R is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl or aralkyl; provided that when R2, R3, and R4 are H; R1 is not hydroxyl or a sugar; further provided that when R4 is hydroxyl, then R1 is not a sugar or hydroxyl, and R1 and R2 are not C=O. [0007] In certain embodiments, R1 is H, hydroxyl, alkoxyl, aryloxy, or amino. In other embodiments, R1 and R2 taken together along with the carbon to which they are bonded, form =0, =N(0R), or =S. In other embodiments, R3 is H and/or R4 is H, alkyl, hydroxyl, aralkyl, -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-N(R)SO2]qR5, -[(W)-C(0)N(R)]qR5, -[(W)-0]qR5, -[(W)-C(0)]qR5, or -[(W)-C(0)0]qR5. In other embodiments, R1 is H or -OR, R2 is H or alkyl, and R4 is H. In others, R2 is H or alkyl, R3 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, or aralkyl; and/or R4 is H, alkyl, aralkyl, -[(W)-N(R)C(0)]qR5, -[(W)-N(R)SO2]qR5, -[(W)-C(0)N(R)]qR5, -[(W)-0]qR5, -[(W)-C(0)]qR5, or -[(W)-C(0)0]qR5. In other embodiments, R1 is sulfonamide
[0008] In another embodiment, the present invention relates to a compound selected from the group consisting of:
Figure imgf000004_0001
Figure imgf000005_0001
Figure imgf000006_0001
Figure imgf000007_0001
or a pharmaceutically acceptable salt thereof.
[0009] In certain embodiments, the compounds mentioned above are isolated. [0010] In another embodiment, the present invention relates to an isolated compound selected from the group consisting of:
Figure imgf000007_0002
or a pharmaceutically acceptable salt thereof.
[0011] In another embodiment, the present invention relates to a compound represented by the following structure:
Figure imgf000008_0001
or a pharmaceutically acceptable salt thereof; wherein R1 is H, alkyl, -OR, amino, sulfonamido, sulfamido, -OC(O)R5, - N(R5)C(O)R5, or a sugar;
R2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, nitrile, or heterocycloalkyl; or R1 and R2 taken together form =0, =S, =N(0R), =N(R), =N(NR2), =C(R)2;
R3 is H, alkyl, alkenyl, or alkynyl;
R4 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR5, -C(O)R5, -CO2R5, -SO2R5, -C(O)N(R5)(R5), -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-C(0)]qR5, -[(W)-C(0)0]qR5, -[(W)-0C(0)]qR5, -[(W)-SO2]qR5, -[(W)-N(R5)SO2]qR5, -[(W)-C(O)N(R5)]qR5, -[(W)-0]qR5, -[(W)-N(R)]qR5, -W-NR5S+X", or -[(W)-S]qR5; wherein each W is, independently, a diradical; each q is, independently, 1, 2, 3, 4, 5, or 6;
X" is a halide; each R is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl or -[C(R)2]P-R6; wherein p is 0-6; or any two occurrences of R5 can be taken together to form a 4-8 membered optionally substituted ring which contains 0-3 heteroatoms selected from N, O, S, and P; each R6 is, independently, hydroxyl, -N(R)COR, -N(R)C(O)OR, -N(R)SO2(R), -C(O)N(R)2, -OC(O)N(R)(R), -SO2N(R)(R), -N(R)(R), -COOR, -C(O)N(OH)(R), -OS(O)2OR, -S(O)2OR, -OP(O)(OR)(OR), -NP(O)(OR)(OR), or -P(O)(OR)(OR); each R is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl or aralkyl; each of R7 and R7 is H; or R7 and R7 taken together form =0;
R8 and R9 are H; or
R and R taken together form a bond; and provided that when R3, R4, R8, R9 are H and R7 and R7 taken together form =0; R1 can not be hydroxyl and R2 can not be H; provided that when R3, R4, R8, R9 are H and, R7 and R7 taken together form =0; R1 can not be acetate and R2 can not be H; provided that when R3, R4, R8, R9 are H and, R7 and R7 are H; R1 and R2 taken together can not be =0; and provided that when R3, R4, R8, R9 are H and, R7 and R7 are H; R1 and R2 can not be H.
[0012] In some embodiments, the compound is epimerically pure and/or isolated. In other embodiments, R4 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR5, -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-C(0)]qR5, -[(W)-C(0)0]qR5, -[(W)-0C(0)]qR5, -[(W)-SO2]qR5, -[(W)-N(R5)SO2]qR5, -[(W)-C(O)N(R5)]qR5, -[(W)-0]qR5, -[(W)-N(R)]qR5, or -[(W)-S]qR5. Each of R7 and R7 can be H. In addition, R1 and R2 taken together form =0.
[0013] In another embodiment, the present invention relates to a compound selected from the group consisting of:
Figure imgf000009_0001
or a pharmaceutically acceptable salt thereof. [0014] In certain embodiments, the above compounds are epimerically pure and/or isolated.
[0015] In another embodiment, the present invention relates to an epimerically pure compound selected from the group consisting of:
Figure imgf000010_0001
or a pharmaceutically acceptable salt thereof.
[0016] Another aspect of the present invention relates to a pharmaceutical composition including any of the aforementioned compounds, and a pharmaceutically acceptable excipient.
[0017] In one embodiment, the present invention relates to a process for preparing cyclopropyl derivatives of cyclopamine and related analogs having the formula 136:
Figure imgf000010_0002
136 wherein
Y is CR7R8;
R1 is H, alkyl, amino, hydroxyl, carboxyl, carbamoyl, alkoxy, hydroxyl, sugar or a protected hydroxyl group;
R2 is H, alkyl, alkenyl, alkynyl, nitnle, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or R1 and R2 taken together form =0, =S, =N(OR9), =N(R9),
=C(R9)2 2,, oorr ==NN((NN((RR99))22));; each of R '3, R "4, a aniidu R K.5 i iss,, i unidueeppeeniidueeniitLliyy,, H n,, a alikκyyli,, a alikκeeniiyyli,, a alikκy; nyl, aryl, cycloalk kyyll,, hheetteerrooccyyccllooaallkkyyll,, aarralkyl, heteroaryl, or heteroaralkyl; or R3 and R4 or R4 and R31 taken together form a bond; R is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR9, -C(O)R9, -CO2R9, -SO2R9, -C(O)N(R9)(R9), -[C(R9)2]qR9, -[(W)-N(R9)C(O)]qR9, -[(W)-C(0)]qR9, -[(W)-C(0)0]qR9, -[(W)-0C(0)]qR9, -[(W)-SO2]qR9, -[(W)-N(R9)SO2]qR9, -[(W)-C(O)N(R9)]qR9, -[(W)-0]qR9, -[(W)-N(R9)]qR9, -[(W)-S]qR9, or a nitrogen protecting group; wherein each W is independently a diradical; each q is independently 1, 2, 3, 4, 5, or 6; each of R7 and R8 is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester; and each R9 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl,aralkyl, heteroaryl, or heteroaralkyl.
[0018] The process includes the steps of contacting a compound of formula 136a with a haloalkylzinc phosphate cyclopropanating agent to yield a compound of formula 136:
Figure imgf000011_0001
136a wherein
R1, R2, R3, R4, R5, R6 are as defined in compound 136.
[0019] In another embodiment, the present invention provides methods for preparing a compound of formula 137:
Figure imgf000011_0002
137 wherein
Y is CR7R8;
R1 is H, alkyl, amino, hydroxyl, carboxyl, carbamoyl, alkoxy, hydroxyl, sugar or a protected hydroxyl group;
R2 is H, alkyl, alkenyl, alkynyl, nitrile, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or R1 and R2 taken together form =0, =S, =N(0R9), =N(R9), =C(R9)2, or =N(N(R9)2); each of R3, R4, and R is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or R3 and R4 or R4 and R5 taken together form a bond;
R is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR9, -C(O)R9, -CO2R9, -SO2R9, -C(O)N(R9)(R9), -[C(R9)2]qR9, -[(W)-N(R9)C(O)]qR9, -[(W)-C(0)]qR9, -[(W)-C(0)0]qR9, -[(W)-0C(0)]qR9, -[(W)-SO2]qR9, -[(W)-N(R9)SO2]qR9, -[(W)-C(O)N(R9)]qR9, -[(W)-0]qR9, -[(W)-N(R9)]qR9, -[(W)-S]qR9, or a nitrogen protecting group; wherein each W is, independently, a diradical; each q is independently 1, 2, 3, 4, 5, or 6; each of R and R is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester; and each R9 is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl,aralkyl, heteroaryl, or heteroaralkyl. The process includes the steps of: first contacting a compound of formula 137a with a haloalkylzinc phosphate cyclopropanating agent;
Figure imgf000012_0001
137a wherein R1, R2, R3, R4, R , R are as defined in compound 137; to form a compound with formula 137b
Figure imgf000013_0001
137b wherein
R1, R2, R3, R4, R , R and Y are as defined in compound 137; and then contacting the compound of formula 137b with an acid to give a compound of formula 137.
[0020] In certain embodiments, R7 and R8 can both be H; in other embodiments R1 can be a protected hydroxyl; and/or R6 is a nitrogen protecting group.
[0021] In certain embodiments, the haloalkylzinc phosphate cyclopropanating agent is formed by combining a phosphoric acid of formula 141a, a dialkylzinc, and a dihaloalkylane of formula 141b:
Figure imgf000013_0002
141a 141b wherein each of X and X' is, independently, chloride, bromide, or iodide; each of R7 and R8 is, independently, H, alkyl, halide, amido, nitro, or ester; each of R10 and R11 is, independently, alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R10 and R11 taken together have the formula 141c, 141d, or 141e;
Figure imgf000014_0001
141c 141d 141e wherein m is, independently for each occurrence, 0, 1, 2, 3, or 4; n is, independently for each occurrence, 0,1, or 2; and each of R12, R13, R14, R15, R16, R17 and R18 is, independently, alkyl, aryl, aralkyl, or halide.
[0022] In another embodiment, the present invention relates to a process for preparing a compound of formula 142:
Figure imgf000014_0002
142
[0023] The process includes the steps of contacting a compound of formula 142a with a cyclopropanating agent to form a compound formula 142b; and
Figure imgf000014_0003
142a
Figure imgf000015_0001
142b combining the compound of formula 142b with an acid to give the compound of formula 142; wherein
7 R 1
Y is CR R ; R is a protected hydroxyl group;
R2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; each of R3, R4, and R5 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
R3 and R4 or R4 and R5 taken together form a bond; R6 is a nitrogen protecting group; each of R7 and R8 is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester; and each R9 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl.
In certain embodiments, R and R can both be H; in other embodiments the protected hydroxyl group can be an ester or a carbonate; the nitrogen protecting can be a
7 R carbamate or an amide; R and R can both be H and the nitrogen protecting can be a carbamate or an amide; R2 and R3 can be H and R4 and R taken together can form a bond; and/or the cyclopropanating agent is generated from a dihaloalkane and a metal species (e.g., dialkyl zinc or a zinc copper couple).
[0024] In certain embodiments the cyclopropanating agent is generated from a dihaloalkane species and a dialkyl zinc species, and a phosphoric acid species or a salt thereof. The phosphoric acid species can have a structure of formula 151:
Figure imgf000016_0001
151 or a salt thereof; wherein each of R10 and R11 is independently alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R10 and R11 taken together have the formula 151a, 151b, or 151c;
Figure imgf000016_0002
wherein m independently for each occurrence is 0, 1, 2, 3, or 4; n independently for each occurrence is 0,1, or 2; each of R12, R13, R14, R15, R16, R17 and R18 is, independently, alkyl, aryl, aralkyl, or halide.
[0025] In certain embodiments the acid is a Bronsted acid (e.g., acetic acid, trifluoromethanesulfonic acid, phosphoric acid, methanesulfonic acid or HCl). In other embodiments the acid is a Lewis acid (e.g., BF3, zinc chloride, zinc methanesulfonate, or a zinc salt).
[0026] The present invention also relates to a process for preparing a compound of formula 156:
Figure imgf000016_0003
156 [0027] The process includes the steps of: contacting a compound of formula 156a with a cyclopropanating agent to form a compound formula 156b; and
Figure imgf000017_0001
156b
combining the compound of formula 156b with an acid to give the compound of formula 156; where R1 is an oxygen protecting group selected from the group consisting of formate, acetate, chloroacetate, dichloroacetate, trichloroacetate, pivaloate, benzoate, alkyl carbonate, alkenyl carbonate, aryl carbonates, aralkyl carbonate, 2,2,2-trichloroethyl carbonate, alkoxymethyl ether, aralkoxymethyl ether, alkylthiomethl ether, aralkylthio ether, arylthio ether, trialkylsilyl ether, alkylarylsilyl ether, benzyl ether, arylmethyl ether, allyl ether; and R2 is a nitrogen protecting group selected from the group consisting of formyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, phenyl acetyl, benzoyls, alkyl carbamates, aralkyl carbamates, aryl carbamates, allyl, aralkyl, triarylmethyl, alkoxymethyl, aralkoxymethyl, N-2-cyanoethyl, diary lphosphinamides, dialkylphosphinamidates, diarylphosphinamidates, and trialkylsilyl. [0028] In certain embodiments the cyclopropanating agent is formed by combining a phosphoric acid of formula 58a, a dialkylzinc, and a dihaloalkylane of formula 158b:
Figure imgf000018_0001
158a 158b wherein each of X and X' is, independently, chloride, bromide, or iodide; each of R and R8 is, independently, H, alkyl, halide, amido, or ester; each of R10 and R11 is, independently, alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R10 and R11 taken together have the formula 158c, 158d, or 158e;
Figure imgf000018_0002
wherein m independently for each occurrence is 0, 1, 2, 3, or 4; n independently for each occurrence is 0,1, or 2; each of R12, R13, R14, R15, R16, R17 and R18 is, independently, alkyl, aryl, aralkyl, or halide.
[0029] The oxygen protecting group can be, in some embodiments, selected from alkyl carbonates, aralkyl carbonates (e.g., benzylcarbonate), benzoates, pivaloate, or formate. The nitrogen protecting group can be selected from benzoyl, trichloroacetyl, trifluoroacetyl, formyl, alkyl carbamates, aralkyl carbamates (e.g., benzylcarbamate), aryl carbamates, diarylphosphinamides, dialkylphosphinamidates, or diarylphosphinamidates.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
[0030] The definitions of terms used herein are meant to incorporate the present state-of-the-art definitions recognized for each term in the chemical and pharmaceutical fields. Where appropriate, exemplification is provided. The definitions apply to the terms as they are used throughout this specification, unless otherwise limited in specific instances, either individually or as part of a larger group.
[0031] As used herein, the definition of each expression, e.g., alkyl, m, n, etc., when it occurs more than once in any structure, is intended to be independent of its definition elsewhere in the same structure.
[0032] The term "acylamino" refers to a moiety that may be represented by the general formula:
O
N u R54
R50 wherein R50 and R54 independently represent a hydrogen, an alkyl, an alkenyl or -(CH2)m-R61, where R61 represents an aryl, a cycloalkyl, a cycloalkenyl, a heterocycle or a polycycle; and m is zero or an integer in the range of 1 to 8.
[0033] The terms "alkenyl" and "alkynyl" refer to unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double or triple bond respectively.
[0034] The terms "alkoxyl" or "alkoxy" refers to an alkyl group, as defined above, having an oxygen radical attached thereto. Representative alkoxyl groups include methoxy, ethoxy, propyloxy, tert-butoxy and the like.
[0035] The term "alkyl" refers to the radical of saturated aliphatic groups, including straight-chain alkyl groups, branched-chain alkyl groups, cycloalkyl (alicyclic) groups, alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In certain embodiments, a straight chain or branched chain alkyl has 30 or fewer carbon atoms in its backbone (e.g., C1-C30 for straight chain, C3-C30 for branched chain), 20 or fewer. Likewise, certain cycloalkyls have from 3-10 carbon atoms in their ring structure, and others have 5, 6 or 7 carbons in the ring structure.
[0036] The term "alkylthio" refers to an alkyl group, as defined above, having a sulfur radical attached thereto. In certain embodiments, the "alkylthio" moiety is represented by one of -S-alkyl, -S-alkenyl, -S-alkynyl, and -S-(CH2)m-R61, wherein m and R61 are defined above. Representative alkylthio groups include methylthio, ethyl thio, and the like.
[0037] The term "amido" is art recognized as an amino-substituted carbonyl and includes a moiety that may be represented by the general formula:
Figure imgf000020_0001
wherein R50 and R51 each independently represent a hydrogen, an alkyl, an alkenyl, -(CH2)m-R61, R61 represents an aryl, a cycloalkyl, a cycloalkenyl, a heterocycle or a polycycle; and m is zero or an integer in the range of 1 to 8, or R50 and R51, taken together with the N atom to which they are attached complete a heterocycle having from 4 to 8 atoms in the ring structure. Certain embodiments of the amide in the present invention will not include imides which may be unstable.
[0038] The terms "amine" and "amino" are art-recognized and refer to both unsubstituted and substituted amines, e.g., a moiety that may be represented by the general formulas:
Figure imgf000020_0002
wherein R50 and R51 (and optionally R52) each independently represent a hydrogen, an alkyl, an alkenyl, or -(CH2)m-R61, where R61 is defined as above. Thus, the term "alkylamine" includes an amine group, as defined above, having a substituted or unsubstituted alkyl attached thereto, i.e., at least one of R50 and R51 is an alkyl group.
[0039] The term "aralkyl", as used herein, refers to an alkyl group substituted with an aryl group (e.g., an aromatic or heteroaromatic group).
[0040] The term "aryl" as used herein includes 5-, 6- and 7-membered single-ring aromatic groups that may include from zero to four heteroatoms, for example, benzene, anthracene, naphthalene, pyrene, pyrrole, furan, thiophene, imidazole, oxazole, thiazole, triazole, pyrazole, pyridine, pyrazine, pyridazine and pyrimidine, and the like. Those aryl groups having heteroatoms in the ring structure may also be referred to as "aryl heterocycles" or "heteroaromatics." The aromatic ring may be substituted at one or more ring positions with such substituents as described above, for example, halogen, azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, sulfonamido, ketone, aldehyde, ester, heterocyclyl, aromatic or heteroaromatic moieties, -CF3, -CN, or the like. The term "aryl" also includes polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings (the rings are "fused rings") wherein at least one of the rings is aromatic, e.g., the other cyclic rings may be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls.
[0041] The term "Bronsted acid" refers to any substance that can act as a hydrogen ion (proton) donor.
[0042] The term "carboxyl" is defined to include esters, thiocarboxyl, aldehydes, ketones and the like and thus includes such moieties as may be represented by the general formulas:
Figure imgf000021_0001
wherein X50 is a bond or represents an oxygen or a sulfur, and each of R55 and R56 represents independently a hydrogen, an alkyl, an alkenyl, -(CH2)m-R61, where m and R61 are defined above.
[0043] The term "diradical" refers to any of a series of divalent groups from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, and heteroaralkyl
groups. For example,
Figure imgf000021_0002
is also an alkyl
diradical; \=/ is an aralkyl diradical; and
Figure imgf000021_0003
is an
(alkyl)heteroaralkyl diradical. Typical examples include alkylenes of general structure (CH2)χ where X is 1-6, and corresponding alkenylene and alkynylene linkers having 2-6 carbon atoms and one or more double or triple bonds; cycloalkylene groups having 3-8 ring members; and aralkyl groups wherein one open valence is on the aryl ring and one is
on the alkyl portion such as \^=> and its isomers.
[0044] The term "haloalkyl", as used herein, refers to an alkyl group where anywhere from 1 to all hydgrogens have been replaced with a halide. A "perhaloalkyl" is where all of the hydrogens have been replaced with a halide.
[0045] The term "heteroatom" as used herein means an atom of any element other than carbon or hydrogen. Examples of heteroatoms include boron, nitrogen, oxygen, phosphorus, sulfur and selenium.
[0046] The terms "heterocyclyl" or "heterocyclic group" refer to 3- to 10- membered ring structures, in some instances from 3- to 7-membered rings, whose ring structures include one to four heteroatoms. Heterocycles can also be polycycles. Heterocyclyl groups include, for example, thiophene, thianthrene, furan, pyran, isobenzofuran, chromene, xanthene, phenoxathiin, pyrrole, imidazole, pyrazole, isothiazole, isoxazole, pyridine, pyrazine, pyrimidine, pyridazine, indolizine, isoindole, indole, indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine, naphthyridine, quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline, phenanthridine, acridine, pyrimidine, phenanthroline, phenazine, phenarsazine, phenothiazine, furazan, phenoxazine, pyrrolidine, oxolane, thiolane, oxazole, piperidine, piperazine, morpholine, lactones, lactams such as azetidinones and pyrrolidinones, sultams, sultones, and the like. The heterocyclic ring may be substituted at one or more positions with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, -CF3, -CN, or the like.
[0047] The term "isolated" in connection with a compound of the present invention means the compound is not in a cell or organism and the compound is separated from some or all of the components that typically accompany it in nature.
[0048] The term "Lewis acid" refers to any substance that can act as an electron pair acceptor. [0049] Unless the number of carbons is otherwise specified, "lower alkyl" as used herein means an alkyl group, as defined above, but having from one to ten carbons, in some embodiments from one to six carbon atoms in its backbone structure. Likewise, "lower alkenyl" and "lower alkynyl" have similar chain lengths. Certain alkyl groups are lower alkyls. In some embodiments, a substituent designated herein as alkyl is a lower alkyl.
[0050] As used herein, the term "nitro" means -NO2; the term "halogen" designates -F, -Cl, -Br or -I; the term "sulfhydryl" means -SH; the term "hydroxyl" means -OH; and the term "sulfonyl" means -SO2-.
[0051] The term "oxo" refers to a carbonyl oxygen (=0).
[0052] The terms "polycyclyl" or "polycyclic group" refer to two or more rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are "fused rings". Rings that are joined through non-adjacent atoms are termed "bridged" rings. Each of the rings of the polycycle may be substituted with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, -CF3, -CN, or the like.
[0053] The term "epimerically pure" in connection with a compound of the present invention means that the compound is substantially free of stereoisomers of the compound wherein the configuration of the stereogenic center that R3 is bonded to is inverted. For example an epimerically pure compound represented by the following formula:
Figure imgf000023_0001
99 wherein R1, R2, R3, R4, R7, R7 , R8, and R9 are as defined below, is substantially free of compounds represented by the following formula:
Figure imgf000024_0001
wherein R1, R2, R3, R4, R7, R7 , R8, and R9 are as defined below. Epimerically pure compounds contain less than about 20 % by mass, less than about 15% by mass, less than about 10% by mass, less than about 5% by mass, or less than about 3% by mass of stereoisomeric compounds wherein the configuration of the stereogenic center that R3 is bonded to is inverted relative to the compound.
[0054] The phrase "protecting group" as used herein means temporary substituents which protect a potentially reactive functional group from undesired chemical transformations. Examples of such protecting groups include esters of carboxylic acids, silyl ethers of alcohols, and acetals and ketals of aldehydes and ketones, respectively. The field of protecting group chemistry has been reviewed (Greene, T. W.; Wuts, P.G.M. Protective Groups in Organic Synthesis, 2nd ed.; Wiley: New York, 1991). In some cases, the functional group being protected and the protecting group are together referred to as one moiety. For example, the fragment shown below is sometimes referred to as a benzyl carbonate; i.e., the protected (underlined) O makes up part of the carbonate.
Figure imgf000024_0002
[0055] Similarly, the fragment shown below, in which the protected N makes up part of the carbamate, is referred to as a benzyl carbamate.
Figure imgf000024_0003
[0056] The term "sugar" as used herein refers to a natural or an unnatural monosaccharide, disaccharide or oligosaccharide comprising one or more pyranose or furanose rings. The sugar may be covalently bonded to the steroidal alkaloid of the present invention through an ether linkage or through an alkyl linkage. In certain embodiments the saccharide moiety may be covalently bonded to a steroidal alkaloid of the present invention at an anomeric center of a saccharide ring. Sugars may include, but are not limited to ribose, arabinose, xylose, lyxose, allose, altrose, glucose, mannose, gulose, idose, galactose, talose, glucose, and trehalose.
[0057] The term "sulfonamido" or "sulfonamide" as used herein includes a moiety having either of the following formulae:
O O
N S R56 S N(R50)2
R50 O O wherein R50 and R56 are as defined above.
[0058] The terms "triflyl", "tosyl", "mesyl", and "nonaflyl" refer to trifluoromethanesulfonyl, p-toluenesulfonyl, methanesulfonyl, and nonafluorobutanesulfonyl groups, respectively. The terms "triflate", "tosylate", "mesylate", and "nonaflate" to trifluoromethanesulfonate ester, p-toluenesulfonate ester, methanesulfonate ester, and nonafluorobutanesulfonate ester functional groups and molecules that contain the groups, respectively.
[0059] The term "thioxo" refers to a carbonyl sulfur (=S).
[0060] It will be understood that "substitution" or "substituted with" includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc.
[0061] Certain compounds of the present invention may exist in particular geometric or stereoisomeric forms. The present invention contemplates all such compounds, including CM- and trans -isomers, R- and 5-enantiomers, diastereomers, (D)- isomers, (L)-isomers, the racemic mixtures thereof, and other mixtures thereof, as falling within the scope of the invention. Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in this invention.
[0062] As set out above, certain embodiments of the present compounds may contain a basic functional group, such as amino or alkylamino, and are, thus, capable of forming pharmaceutically-acceptable salts with pharmaceutically-acceptable acids. The term "pharmaceutically-acceptable salts" in this respect, refers to the relatively non-toxic, inorganic and organic acid addition salts of compounds of the present invention. These salts can be prepared in situ in the administration vehicle or the dosage form manufacturing process, or by separately reacting a purified compound of the invention in its free base form with a suitable organic or inorganic acid, and isolating the salt thus formed during subsequent purification. Representative salts include the hydrobromide, hydrochloride, sulfate, bisulfate, phosphate, nitrate, acetate, valerate, oleate, palmitate, stearate, laurate, benzoate, lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate, tartrate, napthylate, mesylate, glucoheptonate, lactobionate, and laurylsulphonate salts and the like. (See, for example, Berge et al. (1977) "Pharmaceutical Salts", /. Pharm. ScL 66:1-19)
[0063] The pharmaceutically acceptable salts of the compounds of the present invention include the conventional nontoxic salts or quaternary ammonium salts of the compounds, e.g., from non-toxic organic or inorganic acids. For example, such conventional nontoxic salts include those derived from inorganic acids such as hydrochloride, hydrobromic, sulfuric, sulfamic, phosphoric, nitric, and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, palmitic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicyclic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isothionic, and the like.
[0064] In other cases, the compounds of the present invention may contain one or more acidic functional groups and, thus, are capable of forming pharmaceutically- acceptable salts with pharmaceutically-acceptable bases. The term "pharmaceutically- acceptable salts" in these instances refers to the relatively non-toxic, inorganic and organic base addition salts of compounds of the present invention. These salts can likewise be prepared in situ in the administration vehicle or the dosage form manufacturing process, or by separately reacting the purified compound in its free acid form with a suitable base, such as the hydroxide, carbonate or bicarbonate of a pharmaceutically-acceptable metal cation, with ammonia, or with a pharmaceutically- acceptable organic primary, secondary or tertiary amine. Representative alkali or alkaline earth salts include the lithium, sodium, potassium, calcium, magnesium, and aluminum salts and the like. Representative organic amines useful for the formation of base addition salts include ethylamine, diethylamine, ethylenediamine, ethanolamine, diethanolamine, piperazine and the like. (See, for example, Berge et al, supra)
Synthesis of Steroidal Alkaloid Compounds
[0065] The ring expanded steroidal alkaloid derivatives described above can be prepared directly from naturally occurring steroidal alkaloids or synthetic analogs thereof. In certain instances, the steroidal alkaloid starting materials can be cyclopamine or jervine. These steroidal alkaloids can be purchased commercially or extracted from Veratrum Californicum. Briefly, the process of the present invention comprises the steps of cyclopropanating suitable starting steroidal alkaloid derivatives followed by ring expansion rearrangement of the cyclopropyl derivatives. In some instances, it may be desirable to suitably protect or otherwise transform reactive functionalities present on the molecule prior to cyclopropanation. For example, an alcohol present at R1 and a secondary nitrogen present on the fused furano-piperidine ring can both be protected prior to cyclopropanation. In certain embodiments, protecting groups that are efficiently added and removed from the alkaloid, yield intermediates in the synthetic process with improved handling properties and which allow for the efficient purification of the synthetic intermediates formed may be preferred.
[0066] Examples of oxygen protecting groups include, but are not limited to formate, acetate, chloroacetate, dichloroacetate, trichloroacetate, pivaloate, benzoates, alkyl carbonate, alkenyl carbonate, aryl carbonates, aralkyl carbonate (e.g., benzyl carbonate), 2,2,2-trichloroethyl carbonate, alkoxymethyl ether, aralkoxymethyl ether, alkylthiomethl ether, aralkylthio ether, arylthio ether, trialkylsilyl ether, alkylarylsilyl ether, benzyl ether, arylmethyl ether, and allyl ether. [0067] Examples of nitrogen protecting groups include, but are not limited to formyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, phenyl acetyl, benzoyls, benzamides, alkyl carbamates, aralkyl carbamates (e.g., benzyl carbamates), aryl carbamates, allyl, aralkyl, alkoxymethyl, aralkoxymethyl, N-2-cyanoethyl, diary lphosphinamides, dialkylphosphinamidates, diarylphosphinamidates, and trialkylsilyl.
[0068] Additional protecting groups that may be used in the methods of the present invention are described in Green T. W.; Wuts P. G. Protective Groups in Organic Synthesis 3rd Edition, John Wiley & Sons, Inc. 1999.
[0069] A variety of cyclopropanating agents can be used to cyclopropanate the steroidal alkaloid. 1 , 1 -haloalkylmetal complexes and reactive species referred to as carbenoids, are commonly used to cyclopropanate olefins. These reagents are typically made using a diiodoalkane or diazoalkane and a metal or organometalic species such as Et2Zn, JBu3Al, samarium, copper, rhodium, or palladium. In certain embodiments, Et2Zn and diiodomethane are used to generate the 1,1 -haloalkylmetal species.
[0070] The reactivity and the ease of handling of the 1,1 -haloalkylzinc complexes can be modified by the addition of certain reagents, such as acids. It is believed that the addition of an acid to the 1,1 -haloalkylzinc species generates an alkyl zinc mixed salt. In the examples described below a biarylphosphoric acid is combined with diiodomethane and diethylzinc to generate a putative haloalkyl zinc phosphate cyclopropanating agent. A variety of phosphoric acids can be used to generate the putative haloalkylzinc phosphate.
[0071] Other known cyclopropanation methods such as those utilizing sulfur ylides to react with an olefin conjugated to a carbonyl to add a CH2 or CH-alkyl or CH- aryl group, and metal-catalyzed decomposition of diazoalkyl and α-diazo-carbonyl compounds, such as diazomethane and ethyl diazoacetate, can also be used: these methods readily provide cyclopropanes having alkyl, aryl, alkoxycarbonyl (-COOR), or acyl substituents. Additional cyclopropanating agents are described in Masalov et al., Organic Letters (2004) Vol. 6, pp. 2365-8 and Hansen et al., Chem. Comm. (2006) 4838- 40.
[0072] The cyclopropyl ring may be substituted or unsubstituted. In cases where the cyclopropyl ring is substituted, the groups attached to the methylene of the cyclopropane will be installed onto the D ring after rearrangement and ring expansion. [0073] The cyclopropanation reactions may be conducted in an aprotic solvent. Suitable solvents include ethers, such as diethyl ether, 1,2-dimethoxyethane, diglyme, t- butyl methyl ether, tetrahydrofuran and the like; halogenated solvents, such as chloroform, dichlorome thane, dichloroethane, and the like; aliphatic or aromatic hydrocarbon solvents, such as benzene, xylene, toluene, hexane, pentane and the like; esters and ketones, such as ethyl acetate, acetone, and 2-butanone; polar aprotic solvents, such as acetonitrile, dimethylsulfoxide, dimethylformamide, and the like; or combinations of two or more solvents. In a certain embodiments, dichlorome thane is the solvent used for the cyclopropanation when a dialkyl zinc and diiodomethane is used.
[0074] In the examples described below, a solution containing the cyclopropanating agent is prepared by first adding a solution of a phosphoric acid to a solution of diethylzinc, followed by addition of diiodomethane to the reaction solution. The cyclopropanation substrate is then added to this solution. Alternatively, the cyclopropanation agent can be prepared in the presence of the cyclopropanation substrate by changing the order of addition of the reagents. In certain embodiments, the cyclopropanation reaction is conducted by first adding the phosphoric acid to a solution of dialkylzinc, followed by the addition of the cyclopropanation substrate, and finally the dihaloalkane is added. Using this method the cyclopropanating agent is generated under controlled conditions and immediately reacts with the cyclopropanation substrate. The cyclopropanation methods described herein can also be used to cyclopropanate other polycyclic compounds, for example, those with steroidal backbones.
[0075] Following synthesis of the cyclopropanated steroidal alkaloid core, the compound may be derivatized using a variety of functionalization reactions known in the art. Representative examples include palladium coupling reactions to alkenylhalides or aryl halides, oxidations, reductions, reactions with nucleophiles, reactions with electrophiles, pericyclic reactions, radical reactions, installation of protecting groups, removal of protecting groups, and the like.
[0076] In the presence of Lewis or Bronsted acids the cyclopropyl analogs undergo a rearrangement and ring expansion to afford steroidal alkaloid analogs in which the D ring has been expanded by one carbon. [0077] The cyclopropanation and ring expansion can take place in a two-step one reaction vessel process or in a two-step two reaction vessel process. When the cyclopropanation and ring expansion are conducted in the same reaction vessel the acid used to initiate the ring expansion rearrangement is added after completion of the cyclopropanation reaction. Under certain conditions, the zinc salts that are generated in the course of cyclopropanating the steroidal alkaloid can themselves act as Lewis acids to catalyze the ring expansion rearrangement. The reactivity of the zinc salts generated after the cyclopropanation can be modified by the addition of acids to generate more active Lewis acids.
[0078] As described below in the examples section, the methanesulfonic acid is added to the cyclopropanation reaction vessel after completion of the cyclopropanation. Additional examples of suitable acids include, but are not limited to zinc salts, boron compounds, magnesium salts, titanium salts, indium salts, aluminum salts, tin salts, lanthanum salts, trifluoromethanesulfonic acid, diaryloxyphosporic acids, acetic acid, and HCl. In a certain embodiments of the invention the Lewis acid used is a zinc salt or BF3.
[0079] These ring expanded analogs may be further functionalized using a variety of functionalization reactions known in the art. Representative examples include palladium coupling reactions to alkenylhalides or aryl halides, oxidations, reductions, reactions with nucleophiles, reactions with electrophiles, pericyclic reactions, radical reactions, installation of protecting groups, removal of protecting groups, and the like.
Utility of Compounds
[0080] Hedgehog signaling is essential in many stages of development, especially in formation of left-right symmetry. Loss or reduction of hedgehog signaling leads to multiple developmental deficits and malformations, one of the most striking of which is cyclopia.
[0081] Many tumors and proliferative conditions have been shown to depend on the hedgehog pathway. The growth of such cells and survival can be affected by treatment with the compounds of the present invention. Recently, it has been reported that activating hedgehog pathway mutations occur in sporadic basal cell carcinoma (Xie et al. (1998) Nature 391 : 90-2) and primitive neuroectodermal tumors of the central nervous system (Reifenberger et al. (1998) Cancer Res 58: 1798-803). Uncontrolled activation of the hedgehog pathway has also been shown in numerous cancer types such as GI tract cancers including pancreatic, esophageal, gastric cancer (Berman et al. (2003) Nature 425: 846-51, Thayer et al. (2003) Nature 425: 851-56) lung cancer (Watkins et al. (2003) Nature 422: 313-317, prostate cancer (Karhadkar et al (2004) Nature 431 : 707-12, Sheng et al. (2004) Molecular Cancer 3: 29-42, Fan et al. (2004) Endocrinology 145: 3961-70), breast cancer (Kubo et al. (2004) Cancer Research 64: 6071-74, Lewis et al. (2004) Journal of Mammary Gland Biology and Neoplasia 2: 165-181) and hepatocellular cancer (Sicklick et al. (2005) ASCO conference, Mohini et al. (2005) AACR conference).
[0082] For example, small molecule inhibition of the hedgehog pathway has been shown to inhibit the growth of basal cell carcinoma (Williams, et al., 2003 PNAS 100: 4616-21), medulloblastoma (Berman et al., 2002 Science 297: 1559-61), pancreatic cancer (Berman et al., 2003 Nature 425: 846-51), gastrointestinal cancers (Berman et al., 2003 Nature 425: 846-51, published PCT application WO 05/013800), esophageal cancer (Berman et al., 2003 Nature 425: 846-51), lung cancer (Watkins et al., 2003. Nature 422: 313-7), and prostate cancer (Karhadkar et al., 2004. Nature 43J_: 707-12).
[0083] In addition, it has been shown that many cancer types have uncontrolled activation of the hedgehog pathway, for example, breast cancer (Kubo et al., 2004. Cancer Research 64: 6071-4), heptacellular cancer (Patil et al., 2005. 96th Annual AACR conference, abstract #2942 Sicklick et al., 2005. ASCO annual meeting, abstract #9610), hematological malignancies (Watkins and Matsui, unpublished results), basal carcinoma (Bale & Yu, 2001. Human Molec. Genet. 10:757-762 Xie et al., 1998 Nature 391 : 90-92), medulloblastoma (Pietsch et al., 1997. Cancer Res. 57: 2085-88), and gastric cancer (Ma et al., 2005 Carcinogenesis May 19, 2005 (Epub)). As shown in the Examples, the compounds disclosed herein have been shown to modulate the hedgehog pathway, and selected compounds have been shown to inhibit tumor growth. It is therefore believed that these compounds can be useful to treat a variety of conditions, such as various cancers. Pharmaceutical Compositions
[0084] In another embodiment, the present invention provides pharmaceutically acceptable compositions which comprise a therapeutically-effective amount of one or more of the compounds described above, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. The pharmaceutical compositions of the present invention may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, capsules, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; (8) pulmonarily, or (9) nasally.
[0085] Examples of suitable aqueous and nonaqueous carriers which may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
[0086] These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents, dispersing agents, lubricants, and/or antioxidants. Prevention of the action of microorganisms upon the compounds of the present invention may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as aluminum monostearate and gelatin.
[0087] Methods of preparing these formulations or compositions include the step of bringing into association a compound of the present invention with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.
[0088] When the compounds of the present invention are administered as pharmaceuticals, to humans and animals, they can be given per se or as a pharmaceutical composition containing, for example, about 0.1 to 99%, or about 10 to 50%, or about 10 to 40%, or about 10 to 30, or about 10 to 20%, or about 10 to 15% of active ingredient in combination with a pharmaceutically acceptable carrier.
[0089] Actual dosage levels of the active ingredients in the pharmaceutical compositions of the present invention may be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.
[0090] The selected dosage level will depend upon a variety of factors including the activity of the particular compound of the present invention employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion or metabolism of the particular compound being employed, the rate and extent of absorption, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compound employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.
[0091] In general, a suitable daily dose of a compound of the invention will be that amount of the compound which is the lowest dose effective to produce a therapeutic effect. Such an effective dose will generally depend upon the factors described above. Generally, oral, intravenous and subcutaneous doses of the compounds of the present invention for a patient, when used for the indicated effects, will range from about 0.0001 to about 100 mg, or about 0.001 to about 100 mg, or about 0.01 to about 100 mg, or about 0.1 to about 100 mg per, or about 1 to about 50 mg per kilogram of body weight per day.
[0092] The subject receiving this treatment is any animal in need, including primates, in particular humans, and other mammals such as equines, cattle, swine and sheep; and poultry and pets in general.
Exemplification
[0093] The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention.
Example 1
Figure imgf000034_0001
Figure imgf000034_0002
[0094] Recrystallized cyclopamine 2 (14.1 g, 34.0 mmol, 1 eq) is dissolved in anhydrous DCM (70 mL) and anhydrous MeOH (29 mL). The clear solution is cooled, and triethylamine (10.4 g, 102.7 mmol, 3 eq) followed by benzyl chloroformate (6.20 g, 36.3 mmol, 1.1 eq) is added. After the addition is complete, the solution is stirred in the ice bath for 30 mm. Three portions of benzyl chloroformate (3 X 0.35 g, 3.46 mmol, 0.03 eq) are added over the 3 h. The reaction is slowly quenched with water (71 mL), while maintaining the temperature below 20 0C. The mixture is stirred for 15 mm before the layers are settled and separated. The organic layer is dried over sodium sulfate and filtered. The combined filtrate is buffered with anhydrous pyridine (30 mL), concentrated, and solvent exchanged with additional anhydrous pyridine (43 mL) and concentrated.
[0095] The solution of the compound in pyridine (43 mL) is further diluted with additional anhydrous pyridine (85 mL). Trimethylacetyl chloride (8.3 g, 68.7 mmol, 2 eq) is added slowly to the reaction mixture, and the reaction is heated to 45 0C. The reaction is stirred at 45 0C for 30 min. The reaction is cooled and quenched by the addition of anhydrous MeOH (4.5 mL). The quenched reaction mixture is stirred at rt for 40 min and then diluted with toluene (97 mL) and is treated sequentially with water (35 mL) and a 10 wt % aqueous sodium carbonate solution (100 mL). After vigorous stirring, the layers are separated and the organic layer is washed twice with water (2 x 100 mL), dried over sodium sulfate, and filtered. The filter cake is rinsed with toluene (49 mL) and discarded. The combined filtrates are concentrated, and solvent exchanged with concentration to toluene (145 mL) and further concentrating to dryness. The product is recrystallized from toluene and heptane. The crystalline product is isolated by suction filtration, washed with cold heptane and dried to a constant weight to afford 15.1 g of the desired product. Step B
Figure imgf000035_0001
3 4
[0096] Bis(2,6-dimethyphenyl)phosphate (10.65 g, 34.8 mmol, 3.1 eq) is dried by concentration from anhydrous DCM (42 mL) and held under a nitrogen atmosphere. The phosphate is then redissolved in anhydrous DCM (110 mL). In a separate flask, a solution of neat diethylzinc (4.17 g, 33.8 mmol, 3.0 eq) in anhydrous DCM (35 mL) is prepared and cooled to -25 0C. The phosphate solution is slowly transferred to the vessel containing the diethylzinc solution over 1 h, maintaining the temperature at or below -10 0C. The clear ethylzinc phosphate solution is warmed to 0 0C and stirred for 15 min. Diiodomethane (9.25 g, 34.5 mmoles, 3.0 eq) is slowly added to the ethylzinc phosphate solution, maintaining the reaction temperature between 0 and 5 0C. After the addition is complete, the zinc carbenoid solution is stirred for an additional 20 min. [0097] In a separate flask, compound 3 (7.20 g, 11.4 mmol, 1 eq) is dissolved in anhydrous DCM (36 mL) and transferred to the reaction flask. After the addition is complete, the ice bath is removed and the reaction mixture is allowed to warm to rt. After 6 h the contents of the flask are cooled to -53 0C. A solution of methanesulfonic acid (3.38 g, 35.2 mmol, 3.1 eq) in anhydrous DCM (3 mL) is added, maintaining the reaction temperature below -45 0C. After 10 min morpholine (20 g, 230 mmol, 20 eq) is added to the reaction mixture, maintaining the reaction temperature below - 40 0C. The reaction is allowed to warm to rt overnight. The morpholine salts are removed by filtration and the filter cake rinsed with DCM (22 mL). The combined filtrates are washed with 2N aqueous hydrochloric acid (2 x 140 mL), 5 % aqueous sodium bicarbonate (140 mL), 5 % aqueous sodium bicarbonate (70 mL) and 5 % aqueous sodium bisulfite (70 mL), and brine (144 mL). The organic layer is dried over magnesium sulfate and filtered. Without going to dryness, the DCM solution is concentrated and solvent exchanged with methanol (280 mL). The suspension are chilled with an ice bath and stirred for 40 minutes. The solids are isolated by filtration, washed twice with cold methanol (2 x 25 mL), and dried to a constant weight to afford 5.94 g of the desired product. Step C
Figure imgf000036_0001
[0098] In a round bottom flask, compound 4 (11.67 g, 18.1 mmol, 1 eq) and 20 % palladium hydroxide on wet carbon (2.40 g, 1.71 mmol, 0.09 eq) are placed under a nitrogen atmosphere and diluted with EtOAc (115 mL) and toluene (60 mL). The solution is degassed with nitrogen (3X) with evacuation/purge cycles, and the process is repeated for hydrogen. The suspension is vigorously stirred at rt for 1.5 h. The hydrogen atmosphere is replaced with nitrogen. Ethylenediamine (0.57 g, 9.5 mmol, 0.52 eq) is added to the reaction, and the resulting mixture stirred for 20 min. The solution is filtered under nitrogen, and the filtrate is washed with a 2 % (wt/wt) aqueous solution of ethylenediamine (125 mL) then water (130 mL), and then dried over sodium sulfate. The drying agent is removed by filtration and the filtrate is concentrated to dryness under vacuum. The solids that remained are chased with toluene (2 x 55 mL) on the rotary evaporator and the resulting material used without further purification in the next step
[0099] The material from the previous step is dissolved in anhydrous DCM (26 mL). The resulting clear solution is added to a 1 M solution of DIBAL in DCM (65 mL, 65 mmol, 3.6 eq) while maintaining the reaction temperature between -10 and -25 0C. After 30 min the reaction is quenched with acetone (13 mL), maintaining the reaction temperature at or below 0 0C. After stirring the quenched reaction mixture for 17 min, it is added in portions to a flask containing a cold, stirred solution of 20 % (wt/wt) aqueous Rochelle salt (200 mL). The resulting gelatinous suspension is stirred at rt for 15 h. After stirring, the clean layers are separated and the aqueous layer back extracted with DCM (30 mL). The combined organic layers are washed with water (60 mL) and dried over sodium sulfate. The drying agent is removed by filtration and discarded. The filtrate is concentrated under vacuum and solvent exchanged to toluene (225 mL added in portions). The resulting solution is further concentrated to a suspension (50 mL) and diluted with heptane (115 mL). The resulting mixture is heated until turning homogeneous (92 0C). The solution is cooled slowly over 12 h to 15 0C, and then held for 16 additional h. The crystalline product is isolated by suction filtration, washed with heptane (2 x 75 mL) and dried to a constant weight to afford 7.70 g of the desired product.
[0100] A round bottom flask is sequentially charged with the homo-allylic alcohol (7.50 g, 17.6 mmol, 1 eq), aluminum tri-fe?t-butoxide (6.10 g, 24.8 mmol, 1.4 eq), anhydrous toluene ( 115 mL), and 2-butanone (90 g, 1.24 mol, 7 eq). The suspension is heated under a nitrogen atmosphere to 75 0C for 16 h. The reaction temperature is then allowed to cool to 49 0C. Aqueous 20 % (w/w) potassium sodium tartrate solution (226 g) is added to the stirred suspension. The suspension is stirred at rt for 3.5 h. The layers are separated. The organic layer washed with aqueous 20 % Rochelle salt (2 x 250 mL) and water (225 mL), then dried over sodium sulfate and filtered. The residue is rinsed with toluene (30 mL) and discarded. The combined organics are concentrated to dryness. Residual reaction solvents are removed from the material by concentrating from 2- propanol (250 mL added portion-wise) to a final solution mass of 44 g. Solvent exchange from 2-propanol to heptane (275 mL added portion-wise) to a final solution mass is 41 g fully precipitated the desired product. The suspension is diluted with of additional heptane (40 mL), stirred at rt for 1 h, and filtered. The product is washed with n-heptane (17 mL) and dried to afford 5.4 g of the desired product. Step D
Figure imgf000038_0001
[0101] A round-bottom flask is charged with starting material (110 mg, 0.26 mmol, 1 eq) and 10% palladium on carbon (106 mg). The solids are suspended in pyridine (4 mL). The suspension is placed under hydrogen atmosphere (1 atm) and the mixture is stirred overnight at rt. The reaction mixture is filtered through Celite® and the filtrate concentrated in vacuo. The crude material is purified using silica gel flash chromatography ( MeOH/DCM 5:95) to afford 93 mg of the desired compound. ([M+H] = 426.6 m/z).
Example 2
Figure imgf000038_0002
Figure imgf000038_0003
[0102] Cyclopamine 2 (5.02 g, 12.2 mmol, 1.0 eq) is dissolved in anhydrous pyridine (25 mL). DMAP (300 mg, 2.44 mmol, 0.2 eq.) and triethyl amine (5.5 mL, 39.1 mmol, 3.2 eq) are added, followed by BtO-Cbz (10.5 g, 39.1 mmol, 3.2 eq) and heated at 40 0C for 2h. The mixture is cooled to rt, treated with 30 mL water, heated to get a homogeneous solution and allowed to cool to room temp. The white precipitate that formed is collected by filtration, the filter cake is washed with portions of water (3 X 50 mL), and dried in air to afford 9.53 g of crude material which is crystallized from toluene/heptanes (1 :9, 70 mL) to give 6.75 g of the desired product. Step B
Figure imgf000039_0001
[0103] To a solution of diethyl zinc (572 mg, 482 μL, 4.63 mmol, 3.00 eq) in 5.0 mL DCM at -20 0C is added a solution of bis-(2,6-Dimethylphenyl)phosphonc acid (1.42 g, 4.63 mmol, 3.00 eq) in DCM (15 mL) maintaining the reaction temperature below -8 0C . The solution is aged for 15 mm. at 0 0C, neat dnodomethane (1.24 g, 374 μL, 3.00 eq) is added, aged for 15 mm. at 00C before adding a solution of (BisCBzcyclopamine, 1.05 g, 1.54 mmol, 1.0 eq), in DCM (10 mL). The cooling bath is replaced by a water bath at rt and maintained at rt for 4.5 h. The mixture is cooled to -76 0C with a dry ice-acetone bath and treated drop wise with methanesulfonic acid DCM solution (0.6 mL 50% v/v solution 4.63 mmol, 3.0 eq) maintaining the reaction temperature below -74 0C. The mixture is aged for 15- 20 mm. and quenched drop wise with morpholine (2.69 g, 2.70 mL, 20 eq) maintaining the reaction temperature below -65 0C. The cooling bath is removed, the reaction mixture is stirred for 16-18 h., the white precipitate is filtered off, and the filtrate is successively washed with 2.0 M HCl (2 x 20 mL), satd. sodium bicarbonate (2 x 20 mL), water (2 x 20 mL) and brine (20 mL). Dried over magnesium sulfate, concentrated in vacuo to dryness and the crude is purified by silica gel flash chromatography (hexanes/EtOAc 17:3-^4:1) to afford 924 mg (1.33 mmol, 86%) of the desired product. Step C
Figure imgf000040_0001
[0104] To a solution of compound 7 (4.05 g, 5.83 mmol, 1 eq) in a solution of EtOAc:toluene (2:1, 60 mL ) is added of 20% palladium hydroxide on carbon (823 mg, 0.583 mmol, 0.1 eq.). The flask is evacuated and filled with hydrogen three times. The mixture is stirred under an atmosphere of hydrogen for Ih. Neat ethylene diamine (0.38 mL) is added, stirred for Ih., and the catalyst is filtered off. The filter cake is washed twice with EtOAc:toluene (2:1, 12 mL). The combined filtrates are washed with a 2% aqueous solution of ethylene diamine (3 X 20 mL), dried over sodium sulfate and concentrated in vacuo to give 2.46 g as a white crystalline solid. Step D
Figure imgf000040_0002
[0105] A round bottom flask is sequentially charged with the homo-allylic alcohol 8 (7.50 g, 17.6 mmol, 1 eq), aluminum tri-fe?t-butoxide (6.10 g, 24.8 mmol, 1.4 eq), anhydrous toluene (115 mL), and 2-butanone (90 g, 1.24 mol, 7 eq). The suspension is heated under a nitrogen atmosphere to 75 0C for 16 h. The reaction temperature is then allowed to cool to 49 0C. Aqueous 20 % (w/w) potassium sodium tartrate solution (226 g) is added to the stirred suspension. The suspension is stirred at rt for 3.5 h. The layers are separated. The organic layer washed with aqueous 20 % Rochelle's salt (2 x 250 mL) and water (225 mL), then dried over sodium sulfate and filtered. The residue is rinsed with toluene (30 mL) and discarded. The combined organics are concentrated to dryness. Residual reaction solvents are removed from the material by concentrating from 2-propanol (250 mL added portion- wise) to a final solution mass of 44 g. Solvent exchange from 2-propanol to H-heptane (275 mL added portion-wise) to a final solution mass of 41 g fully precipitated the desired product. The suspension is diluted with of additional H-heptane (40 mL), stirred at rt for 1 h, and filtered. The product is washed with H-heptane (17 mL) and dried to afford 5.4 g of the desired product. Step E
Figure imgf000041_0001
[0106] A round-bottom flask is charged with starting material (110 mg, 0.26 mmol, 1 eq) and 10% palladium on carbon (106 mg). The solids are suspended in pyridine (4 mL). The suspension is placed under hydrogen atmosphere (1 atm) and the mixture is stirred overnight at rt. The reaction mixture is filtered through Celite® and the filtrate concentrated in vacuo. The crude material is purified using silica gel flash chromatography ( MeOH/DCM 5:95) to afford 93 mg of the desired compound. ([M+H] = 426.6 m/z).
Example 3
Figure imgf000041_0002
Figure imgf000041_0003
[0107] In a seal tube, ketone 6 (85 mg, 0.199 mmol, 1 equiv.) was charged and triethyleneglycol (2 mL) was added followed by hydrazine monohydrate (500 mg, 10 mmol, 50 equiv.) and potassium carbonate (138 mg, 1 mmol, 5 equiv.). The tube was sealed and the reaction was heated at 150 0C for 16 h. The reaction was cooled to rt and water was added. The residue was extracted with chloroform (3X). The combined organic layers are washed with water, dried over Na2SO4, and concentrated to dryness. The colorless oil was purified using silica gel flash chromatography (DCM/MeOH 96:4). The purified fractions are pooled and concentrated to dryness. The resulting oil was dissolved in MTBE and washed with water (2X), 2N NaOH, and then brine. The combined organic layers are dried over Na2SO4, filtered and evaporated to afford 64 mg of the desired material as a white foam. ([M+H] = 412.7 m/z).
Example 4
Figure imgf000042_0001
10
Figure imgf000042_0002
5 10
[0108] A sealed tube was charged with compound 5 (223 mg, 0.52 mmol, 1 eq) and DMF (ImL). 2-bromopropane (1.3 g, 10.5 mmol, 20 eq) and Na2CO3 (73 mg, 0.68 mmol, 1.3 eq) were added and the flask was sealed and heated to 50 0C. The mixture was stirred for 16 h at which point -70% conversion was observed. Additional (0.26 g, 2.12 mmol, 4 eq) was added. The reaction was stirred for 2 h and additional 2-bromopropane (0.13 g, 1.1 mmol, 2 eq) was added. The reaction was stirred for another Ih. The reaction was cooled to rt and water was added. The residue was extracted with MTBE (3X). The organic layers were combined washed with brine, dried over Na2SO4, filtered, and concentrated to dryness. The white foam was purified using silica gel flash chromatography (DCM/MeOH 99:1) to give 206 mg of the N-isopropyl derivative as a white foam.
[0109] The N-isopropyl derivative (205 mg, 0.44 mmol, 1 eq) was dissolved in of 4- methoxypyridine (1.5 mL). The flask was placed under inert atmosphere and Pd/C 10% (wet, Aldrich Degussa type ElOl, 40 mg) was added. The flask was sealed and purged three times with hydrogen and left 16 h under 1 atm of hydrogen. Celite® was added to the reaction mixture. The mixture was filtered through a small pad of Celite® and washed with EtOAc. The organic layer was washed with IN HCl aq. (2x) then with water. The organic layer was dried over Na2SO4, filtered though cotton and evaporated to give 34 mg of crude. The aqueous layer was neutralized with 2N KOH and extracted with DCM (3X). The combined organic layers were washed with water, dried over Na2SO4, filtered though cotton and combined with the initial 34 mg of crude. The crude material was purified using silica gel flash chromatography hexane/EtOAc (6:4) to afford 80 mg of desired product. ([M+H] = 468.7 m/z).
Example 5
Figure imgf000043_0001
11
MeOH
Figure imgf000043_0002
Figure imgf000043_0003
6 11
[0110] In a round-bottom flask, compound 6 (88 mg, 0.21 mmol, 1 eq) was dissolved in anhydrous THF (1 mL). The mixture was cooled to 0 0C. Pyridine (84 μL, 1 mmol, 5 eq) and benzoylperoxide (150 mg, 0.62 mmol, 3 eq) were added successively. The homogeneous mixture was gradually warmed to rt over 2 h and stirred overnight at rt. The reaction was quenched by adding saturated NaHCCb. The residue was extracted with MTBE. The combined organic layers were washed with water, dried over Na2SO4, filtered and concentrated under reduced pressure. The crude was purified using silica gel flash chromatography (hexane/EtOAc (9:1 to 4: 1)) to give the N-O derivative product (60 mg, 0.11 mmol) as a white foam. This foam was dissolved in 2 mL of MeOH followed by 2N aqueous KOH (0.4 mL). The reaction mixture was stirred for Ih. Most of the MeOH was evaporated under a stream of nitrogen and IN HCl (500 μL) was added. The material was extracted with DCM (3X). The combined organic layers were washed with water, dried over Na2SO4, filtered and concentrated under reduced pressure. The crude was purified using silica gel flash chromatography (hexanes/EtOAc (from 88:12-M :1)) to yield 11 mg of the desired product. ([M+H] = 442.5 m/z).
Example 6
Figure imgf000044_0001
12
Figure imgf000044_0002
[0111] In a round bottom flask, compound 6 (89 mg, 0.209 mmol, 1 eq) and N- (benzyloxycarbonyl)-aminoacetaldehyde (148 mg, 0.85 mmol, 4 eq) were dissolved in DCM (2 mL ). Sodium tnacetoxyborohydride (177 mg, 0.85 mmol, 4 eq) was added and the reaction was stirred for 3 h at rt. The mixture was poured in saturated aqueous ΝaHCU3 solution and the residue was extracted with DCM (3x). The combined organic layers were washed with water, dried over Na2SO4, filtered though cotton and evaporated to give a foamy solid (247 mg). The crude was dissolved in EtOAc (2 mL) and treated with of 4M HCl (156 μL). After 30 mm a white precipitate slowly formed. The resulting slurry was stirred for 15 mm. Filtration gave 120 mg of white solid. The material was dissolved in EtOAc and treated with a saturated aqueous NaHCU3 solution. The organic layer was collect and the aqueous layer and was extracted with EtOAc (2X). The combined organic layers were washed with brine, dried over Na2SO4. Filtration and evaporation gave the desired intermediate. This material was used in the next step without purification. Step B
Figure imgf000045_0001
13 14
[0112] All of the material from Step A was dissolved in EtOAc (3 mL) and treated with of Pd/C 10% (30 mg , wet,Aldnch Degussa type ElOl). The flask was sealed and purged three times with hydrogen and left overnight under 1 atm of hydrogen. After 16 h, the mixture was filtered through a small pad of Celite® and washed with EtOAc to afford 52 mg of the amine as a white foam. Step C
Figure imgf000045_0002
14 12
[0113] A round-bottom flask containing the amine 14 (52 mg, 0.11 mmol, 1 eq) was charged with the lH-tetrazole-5 -acetic acid (21 mg, 0.166 mmol, 1.5 eq), DCM (2 mL), EDCI (42 mg, 0.22 mmol, 2 eq) and N,N-dnsopropylethylamine (57 mg, 0.44 mmol, 4 eq) The resulting yellow solution was stirred at rt for 4 h. The reaction was quenched by the addition of saturated aqueous NaHCU3 solution and the residue was extracted with DCM (3X). The combined organic layers were dried over Na2SO4, filtered though cotton and evaporated to give 62 mg of off-white solid. This material was purified using silica gel flash chromatography (MeOH/DCM 5:95^10:90) to afford 31 mg of the desired product. ([M+H] = 579.7 m/z).
Example 7
Figure imgf000045_0003
15
Figure imgf000046_0001
[0114] A round-bottom flask was charged with starting material (47 mg, 0.110 mmol, 1 eq) and potassium carbonate (150 mg, 1.09 mmol, 10 eq). The solids were suspended in 2 mL of DCM. Iodomethane (14 μL, 0.22 mmol, 2 eq) was added and the mixture was stirred for 2 at rt. TLC (DCM/MeOH 95:5) indicate >90% completion. Iodomethane (14 μL, 0.22 mmol, 2 eq) was added to the reaction mixture, which was stirred for 2 h. The reaction mixture was added water. The phases were separated and the organics were dried and concentrated to dryness. The residue was purified using silica gel flash chromatography (DCM/MeOH 100:0^98:2) afford 34 mg of the desired product ([M+H] = 440.5 m/z).
Example 8
Figure imgf000046_0002
16
Figure imgf000046_0003
[0115] A round-bottom flask was charged with starting material (59 mg, 0.126 mmol, 1 eq) and potassium carbonate (350 mg, 2.5 mmol, 20 eq). The solids were suspended in 3 mL of DCM. The reaction was charged with iodomethane (80 μL, 1.29 mmol, 10 eq) and the mixture was stirred overnight at rt. The reaction mixture was charged with water. The organic phase was separated and the aqueous layer was back extracted with DCM. The combined organic layers were dried and concentrated to dryness. The residue was purified using silica gel flash chromatography. DCM/MeOH (95:5^90:10) to afford 52 mg of the desired product. ([M+H] = 639.5 m/z). Example 9
Figure imgf000047_0001
17
Figure imgf000047_0002
[0116] In a round bottom flask, compound 5 (50 mg, 0.12 mmol, 1 eq) and N-(t- butoxycarbonyl)-aminoacetaldehyde (6 mg, 0.38 mmol, 3.1 eq) were dissolved in DCM (2 mL ). Sodium triacetoxyborohydride (8 mg, 0.38 mmol, 3.1 eq) was added and the reaction was stirred for 2 h at rt. The mixture was poured in saturated aqueous ΝaHCU3 solution and the residue was extracted with DCM (3x). The combined organic layers were washed with water, dried over Na2SO4, filtered though cotton and evaporated to give a foamy solid (95 mg). The crude material was purified using silica gel flash chromatography (EtOAc/Hexanes 1 : 1) to yield 55 mg of compound 18. Step B
DCM
Figure imgf000047_0004
Figure imgf000047_0003
18 19
[0117] A round-bottom flask was charged with starting material 18 (800 mg, 1.4 mmol, 1 eq). The solid was dissolved in a solution of DCM and TFA (10 mL, 1 :1). The solution was stirred for 45 mm at rt. The reaction was partitioned between a solution of 10% sodium carbonate and DCM. The organic was separated and washed with 10% sodium carbonate. The organic phase was concentrated to dryness. The residue was used without further purification for the next step.
Figure imgf000048_0001
[0118] A round-bottom flask was charged with starting material (300 mg, 0.64 mmol, 1 eq) was dissolved in THF/ ACN (1 :1, 4 mL). The reaction was charged 37% formaldehyde in water (240 μL, 3.22 mmol, 5 eq) and sodium cyanoborohydride (64 mg, 1 mmol, 1.6 eq). The mixture was stirred for 30 min at rt. The reaction was then partitioned between a solution a saturated aqueous solution of sodium bicarbonate and DCM. The organic was separated, dried and concentrated to dryness. The crude material was purified using silica gel flash chromatography (MeOH/DCM 5:95^10:90) to give the desired material. Step D
Figure imgf000048_0002
[0119] A round-bottom flask was charged with starting material 20 (30 mg, 0.06 mmol, 1 eq) and 10% palladium on carbon (30 mg). The solids were suspended in pyridine (2 mL). The suspension was placed under hydrogen atmosphere and the mixture was stirred overnight at rt. The reaction mixture was filtered on Celite® and the filtrate concentrated to dryness. The crude material was purified using silica gel flash chromatography (MeOH/DCM 5:95^10:90) to gave the desired material. ([M+H] = 497.7 m/z).
Example 10
Figure imgf000048_0003
21
Figure imgf000049_0001
[0120] A round-bottom flask was charged with starting material (85 mg, 0.20 mmol, 1 eq) was dissolved in DCM (4 mL). The reaction was charged with N-(2-oxoethyl)acetamide (80 mg, 0.70 mmol, 3.5 eq) and sodium triacetoxyborohydride (170 mg, 0.80, 4 eq). The mixture was stirred for 1 hour at rt. The reaction was partitioned between a solution a saturated aqueous solution of sodium bicarbonate and DCM. The organic was separated, dried and concentrated to dryness. The crude material was purified using silica gel flash chromatography (MeOH/DCM 5:95) to give the desired material. ([M+H] = 511.7 m/z).
Example 11
Figure imgf000049_0002
22
[0121] Compound 22 was synthesized according to the procedure described in example 9, using N-methyl-N-(2-oxoethyl)acetamide in place of N-(2-oxoethyl)acetamide. ([M+H] = 525.7 m/z).
Example 12
Figure imgf000049_0003
23
[0122] Compound 23 was synthesized according to the procedure described in example 10, using N-(2-oxoethyl)-3-phenylpropanamide in place of N-(2-oxoethyl)acetamide. ([M+H] = 601.8 m/z). Example 13
Figure imgf000050_0001
24
[0123] Compound 23 was synthesized according to the procedure described in example 10, using N-methyl-N-(2-oxoethyl)-3-phenylpropanamide in place of N-(2- oxoethyl)acetamide. ([M+H] 615.9 m/z)
Example 14
Figure imgf000050_0002
25
Step A
Figure imgf000050_0003
[0124] A round-bottom flask was charged with compound 6 (4.23 g, 9.94 mmol, 1 eq) and THF (60 mL). Triethylamine (6.92 mL, 49.7 mmol, 5.0 eq) and benzyl chloroformate (1.54 mL, 10.93 mmol, 1.1 eq) were added and the mixture was stirred for 1 hour at rt. The reaction mixture was partitioned between saturated aqueous bicarbonate (100 mL) and EtOAc (100 mL). The phases were separated and the organics were dried (Νa2SO4) and concentrated to dryness. The crude material was purified using silica gel flash chromatography (EtOAc/Hexanes 2:98^14:86) to give 3.75g of material. Step B
Figure imgf000051_0001
[0125] A MeOH solution (10 ml) of cerium trichloride heptahydrate (260 mg, 0.69 mmol, 1.3 eq.) at 0 0C was treated with sodium borohydride (24 mg, 0.65 mmol, 1.2 eq), stirred for 15 mm, and then cooled to -78 0C. A THF solution (10 ml) of ketone 26 (300 mg, 0.54 mmol, 1 eq) was added, and the mixture was stirred for 1 h and then warmed to rt. Water (50 ml) and EtOAc (50 ml) were added, mixed, and the layers split. The organic layer was collected, washed with brine (30 ml), dried over sodium sulfate, and concentrated to a white residue. The crude product was purified by silica gel flash chromatography (ether/hexanes 2:3-» 1: 1) to give 235 mg of 3-beta alcohol 27. Step C
Figure imgf000051_0002
[0126] Compound 27 (235 mg, 0.42 mmol, 1 eq) was dissolved in EtOAc (7 ml) in a flask with stir bar and rubber septum. The solution was sparged with nitrogen, and Pd/C 10% (wet,Aldnch Degussa type ElOl, 50 mg) was added. This mixture was sparged with nitrogen and then hydrogen gas and stirred at rt for 3h. The mixture was then sparged with nitrogen, filtered through a 0.45 μm polyethylene membrane and concentrated to a clear oil. The oil was purified by silica gel flash chromatography (NH40H(aq)/Me0H/DCM 0.5:2:97.5^0.5:6:93.5) to give 130 mg of compound 25 as a white powder. ([M+H] = 427.4 m/z) Example 15
Figure imgf000052_0001
28
Step A
Figure imgf000052_0002
[0127] A THF solution (10 ml) of ketone 26 (300 mg, 0.54 mmol, 1 eq) at -78 0C was treated with K-Selectnde® (Potassium tri-sec-butylborohydride) (0.58 ml, 0.58 mmol, 1.1 eq) and stirred for 60 mm. Methanol (1 ml) was added and the solution warmed to rt. Water (50 ml) and EtOAc (50 ml) were added, mixed, and the layers split. The organic layer was washed with brine (30 ml), dried over sodium sulfate, and concentrated to a white residue. The crude product was purified by silica gel flash chromatography (Ether/Hexanes 2:3^ 1:14) to give 170 mg of pure 3 -alpha alcohol 29. Step B
Figure imgf000052_0003
[0128] Compound 29 (170 mg, 0.30 mmol, 1 eq) was dissolved in EtOAc (5 ml) in a flask with stir bar and rubber septum. The solution was sparged with nitrogen, and Pd/C 10% (wet, Aldrich Degussa type ElOl, 35 mg) was added. This mixture was sparged with nitrogen and then hydrogen gas and stirred at rt for 3h. The mixture was then sparged with nitrogen, filtered through a 0.45 μm polyethylene membrane and concentrated to a clear oil. The oil was purified by silica gel flash chromatography (NH40H(aq)/Me0H/DCM 0.5:2:97.5^0.5:6:93.5) to afford 76 mg of compound 28 as a white powder ([M+H] = 427.4 m/z).
Example 16
Figure imgf000053_0001
30
Step A
Figure imgf000053_0002
[0129] Compound 27 (100 mg, 0.18 mmol, 1 eq) with benzyltnethylammonium chloride (8 mg, 0.36 mmol, 0.2 eq) was dissolved in DCM (5 ml) and stirred vigorously with dimethyl sulfate (130 μL, 1.43 mmol, 8 eq) and 50% aqueous potassium hydroxide (0.5 ml) at rt for 18h. The mixture was partitioned between water (30 ml) and EtOAc (30 ml), and the organic layer was then washed with brine, dried over sodium sulfate, and concentrated to a clear oil. The crude ether was purified by silica gel flash chromatography (Ether/Hexanes 3:7-^9: 113) to give 75 mg of the methyl ether as a clear oil. Step B
Figure imgf000053_0003
[0130] Compound 31 (66 mg, 0.115 mmol, 1 eq) was dissolved in EtOAc (5 ml) in a flask with stir bar and rubber septum. The solution was sparged with nitrogen, and Pd/C 10% (wet, Aldrich Degussa type ElOl, 20 mg) was added. This mixture was sparged with nitrogen and then hydrogen gas and stirred at rt for 3h. The mixture was then sparged with nitrogen, filtered through a 0.45 μm polyethylene membrane and concentrated to a clear oil. The oil was punfied by silica gel flash chromatography (NH40H(aq)/Me0H/DCM 0.5:2:97.5^0.5:6:93.5) to give 22 mg of compound 30 as a white powder ( [M+H] = 441.4 m/z).
Example 17
Figure imgf000054_0001
32
DIPEA
Figure imgf000054_0002
Figure imgf000054_0003
[0131] Compound 27 (100 mg, 0.18 mmol, 1 eq) was dissolved in DCM (5 ml), and A- dimethylaminopyndine (4 mg, 0.35 mmol, 0.2 eq), N,N-dnsopropylethylamine (0.15 ml, 0.9 mmol, 5 eq), and acetic anhydride (0.070 ml, 0.72 mmol, 4 eq) were added. After stirring for 12h at rt, the solution was split between EtOAc (30 ml) and 5% aqueous sodium bicarbonate (15 ml). The organic layer was washed with brine, dried over sodium sulfate, and concentrated to a clear oil. The crude ester was purified by silica gel chromatography (Ether/Hexanes 3:7->9:113) to give 100 mg of the ester as a clear oil. Step B
Figure imgf000054_0004
[0132] Compound 33 (100 mg, 0.18 mmol, 1 eq) was dissolved in EtOAc (5 ml) in a flask with stir bar and rubber septum. The solution was sparged with nitrogen, and Pd/C 10% (wet, Aldrich Degussa type ElOl, 20 mg) was added. This mixture was sparged with nitrogen and then hydrogen gas and stirred at rt for 3h. The mixture was then sparged with nitrogen, filtered through a 0.45 μm polyethylene membrane and concentrated to a clear oil. The oil was purified by silica gel flash chromatography (NH40H(aq)/Me0H/DCM 0.5:2:97.5^0.5:6:93.5) to give 45 mg of compound 32 as a white powder ( [M+H] = 469.4 m/z).
Example 18
Figure imgf000055_0001
34
[0133] Compound 34 was synthesized according to the procedure described in example 16, using compound 29 in place of compound 27. ([M+H ] = 441.4 m/z).
Example 19
Figure imgf000055_0002
35
[0134] Compound 34 was synthesized according to the procedure described in example 17, using compound 29 in place of compound 27. MS ([M+H] = 469.4 m/z)
Example 20
Figure imgf000055_0003
36
Figure imgf000056_0001
[0135] An ethanol solution (5 ml) of compound 26 (185 mg, 0.3 mmol, 1 eq) was treated with hydroxylamine hydrochlonde (140 mg, 2 mmol, 6 eq), sodium acetate (160 mg, 2 mmol, 6 eq), and water (0.5 mL), and the mixture was stirred at rt for 1 hr. The mixture was split between EtOAc and water (50 mL each). The organic layer was washed with brine (30 mL), dried over sodium sulfate, and concentrated to a white residue. The crude product was purified by silica gel chromatography (ether/hexanes 2:3 -> 1 :1) to give 193 mg of oxime 37. Step B
Figure imgf000056_0002
[0136] Compound 37 (65 mg, 0.113 mmol) was dissolved in EtOAc (7 ml) in a flask with stir bar and rubber septum. The solution was sparged with nitrogen, and Pd/C 10% (wet,Aldnch Degussa type ElOl, 20 mg) was added. This mixture was sparged with nitrogen and then hydrogen gas and stirred at rt for 3h. The mixture was then sparged with nitrogen, filtered through a 0.45 μm polyethylene membrane and concentrated to a clear oil. The oil was purified by silica gel flash chromatography (NH40H(aq)/Me0H/DCM 0.5:2:97.5->0.5:6:93.5) to give 15 mg of compound 36 as a white powder, a mixture of cis and trans oxime isomers ( [M+H] = 440.3 m/z).
Example 21
Figure imgf000056_0003
38
Figure imgf000057_0001
[0137] Compound 27 (42 mg, 0.075 mmol, 1 eq) was dissolved in DCM (5 ml), and 4- dimethylaminopyridine (2 mg, 0.02 mmol, 0.2 eq), N-Cbz glycine (23 mg, 0.110 mmol, 1.5 eq), and diisopropylcarbodiimide (0.023 ml, 0.150 mmol, 2 eq) were added. After stirring for 12h at rt, the solution was split between EtOAc (30 ml) and 5% aqueous sodium bicarbonate (15 ml). The organic layer was washed with brine, dried over sodium sulfate, and concentrated to a clear oil. The crude ester was purified by silica gel flash chromatography (ether/hexanes 2:3 -> 1:1) to give 35 mg of the ester as a clear oil Step B
Figure imgf000057_0002
[0138] Compound 39 (235 mg, 0.42 mmol, 1 eq) was dissolved in EtOAc (7 mL) in a flask with stir bar and rubber septum. The solution was sparged with nitrogen, and Pd/C 10% (wet,Aldrich Degussa type ElOl, 50 mg) was added. This mixture was sparged with nitrogen and then hydrogen gas and stirred at rt for 3h. The mixture was then sparged with nitrogen, filtered through a 0.45 μm polyethylene membrane and concentrated to a clear oil. The oil was purified by silica gel flash chromatography (NH4OH(aq)/MeOH/DCM 0.5:2:97.5->0.5:6:93.5) to give 17 mg of the desire product as a white powder ( [M+H] = 452.4 m/z).
Example 22
Figure imgf000057_0003
40
[0139] Compound 40 was synthesized according to the procedure described in example 21, using compound 29 in place of compound 27. ([M+H] = 452.4 m/z)
Example 23
Figure imgf000058_0001
41
[0140] Compound 41 was synthesized according to the procedure described in example 10, using N-(2-oxoethyl)-2-phenylacetamide in place of N-(2-oxoethyl)acetamide. ([M+H] = 587.7 m/z).
Example 24
Figure imgf000058_0002
42
Figure imgf000058_0003
[0141] A round-bottom flask was charged with alcohol 29 (7.60 g, 13.53 mmol, 1 eq) and was dissolved in DCM (115 mL). The reaction was charged with triethylamine (8.21 g, 81 mmol, 6.0 eq). The mixture was cooled to 00C and charged with methanesulfonylchloride (1.86 g, 16.2 mmol, 1.2 eq). After 30 min, the reaction mixture was partitioned between a saturated aqueous solution of sodium bicarbonate and EtOAc. The organic layer was separated, dried over sodium sulfate and concentrated to dryness. The residue was purified using silica gel flash chromatography (EtOAc/hexanes 10 -^ 25%) gave the desired material mesylate.
[0142] A round-bottom flask was charged with the mesylate (9.1 g, 14.22 mmol, 1 eq) and was dissolved in 50 mL of DMPU. The reaction was charged with sodium azide (4.62 g, 71.1 mmol, 5.0 eq) and heated to 600C. The mixture was stirred for 17 h. The reaction mixture was then cooled to rt and charged with water. The mixture was stirred for 30 min. The mixture was filtered under vacuum, rinsed with water and air dried and used directly without purification in the next step. Step B
Figure imgf000059_0001
[0143] A round-bottom flask was charged with azide 43 (8.35 g, 14.23 mmol, 1 eq) and THF (120 mL) was added. The reaction was then charged with triphenylphosphine (11.2 g, 42.7 mmol, 3.0 eq). The mixture was heated to 500C and stirred for 20 h. The reaction mixture was then cooled to rt and the solvent removed under vacuum. The residue purified using silica gel flash chromatography (MeOH/DCM 10% -> 20%) to afford the amine.
[0144] A round-bottom flask was charged with the amine (5.10 g, 9.09 mmol, 1 eq) and was dissolved in DCM (60 mL). The reaction was charged with N,N- diisopropylethylamine (5.88 g, 45.5 mmol, 5.0 eq). The mixture was cooled to 00 C and charged with methanesulfonylchloride (2.08 g, 18.2 mmol, 2.0 eq). After 30 minutes, the reaction mixture was partitioned between a saturated aqueous solution of sodium bicarbonate and EtOAc. The organic layer was collected, dried over sodium sulfate and concentrated to dryness. The residue was purified using silica gel flash chromatography (EtOAc/hexanes 10 -> 30%) to afford the Cbz protected methanesulfonamide.
Figure imgf000060_0001
44 42
[0145] A round-bottom flask was charged with the Cbz protected methanesulfonamide (5.37 g, 8.41 mmol, 1 eq) and 10% palladium on carbon (1.0 g). The solids were suspended in 2-propanol (50 mL). The suspension was placed under hydrogen atmosphere and the mixture was stirred for 4 h at 25° C. The reaction mixture was then filtered on Celite® and the filtrate concentrated to dryness. The residue was then purified using silica gel flash chromatography (DCM/MeOH 0 -> 5%) to afford the desired product. [M+H] = 505.6 m/z. Alternate Synthesis of Compound 42
Figure imgf000060_0002
24a
[0146] Recrystallized cyclopamine (2.07 g) is charged to an appropriately sized reaction vessel and placed under an inert atmosphere. EtOAc (7.6 g), triethylamine (1.53 g), and DMAP (307 mg) are added sequentially. The suspension is warmed to 4O0C. Cbz-OBt is added in three portions over 90 minutes, keeping the internal temperature below 450C. The reaction mixture is stirred at 4O0C for 90 minutes. The temperature is maintained while methanol (26.4 g) is slowly added to the reaction mixture. The resulting suspension is cooled to room temperature and stirred for at least 15 hours. The crude product is collected by filtration and rinsed with methanol (5 g). The white solid is dried under vacuum to a constant weight and recrystallized from heptane (30.3 g) and toluene (3.2 g) to afford Compound 24a (3.0 g).
Figure imgf000061_0001
24a 24b
[0147] Solid bis(2,6-dimethylphenyl) hydrogenphosphate and 24a are pre-dried and placed under a nitrogen atmosphere. Neat diethyl zinc (722 mg) is charged to an appropriately sized reaction vessel containing DCM (9.0 g). DCM solutions of the phosphate (1.83 g in 17.9 g) and IPI-332690 (1.34 g in 3.6 g) are added sequentially at or below 25 0C. Diiodomethane (1.58 g) is charged and the reaction is stirred at 28°C for 4-6 hours. The reaction is cooled to -45°C and a solution of methanesulfonic acid in DCM (566 mg in 1.5 g) is charged. After 15 minutes, morpholine (1.711 g) is added and the mixture is allowed to warm to room temperature overnight. The organic layer is washed twice with 2N HCl (2 x 13.6 g) then sequentially with 4.8 wt % sodium carbonate (aq), 4.8 wt% sodium sulfite (aq), and 4.8 wt% brine (13.6 g each). The organic layer is dried, filtered, concentrated to 4 g and diluted with isopropanol (4 g). The product is crystallized from solution by the slow addition of methanol (9.3 g). Filtration with a methanol rinse (2.6 g) and drying afford 1.09 g of 24b (79% isolated yield).
Figure imgf000061_0002
[0148] Johnson Matthey Pd/C catalyst A-305038-5 (890 mg) is charged to an appropriately sized reaction vessel, followed by 24b (2.24 g). The reaction vessel is purged with N2 and toluene (21.8 g) and 2-propanol (6.7 g) are added sequentially. The system is degassed and placed under a nitrogen atmosphere, and the process is repeated with hydrogen. The system is stirred vigorously and the hydrogen blanket is maintained at one atmosphere for 4-5 hours. The reaction is monitor by either TLC or HPLC. If incomplete, the reaction is inerted, additional catalyst (145 mg) is charged, and the hydrogen atmosphere is returned for another hour. Ethylenediamine (12.9 mg) is charged and the mixture was stirred for 15 minutes. The catalyst is removed by filtration with a toluene:IPA (3:1) rinse. The filtrate and rinses are concentrated and solvent exchanged to toluene. The product is crystallized from toluene (19.0 g) and heptane (18.0 g) to afford 24c as a white crystalline solid (1.34 g, 98% yield).
Figure imgf000062_0001
24c 24d
[0149] 24c (644 mg) is charged to an appropriately sized reaction vessel followed by aluminum t-butoxide (525 mg), toluene (8.34 g, 15 vol), and 2-butanone (7.83 g, 15 vol). The contents of the flask are degassed with evacuation/nitrogen purge cycles to remove oxygen and the reaction mixture is heated at 75°C with vigorous stirring for 16-18 hours. The reaction is quenched by the addition of aqueous Rochelle's salt (2.6 g in 10.3 g water) and the mixture vigorously stirred for one hour at 45 0C. The aqueous and organic layers are separated. The aqueous layer is back extracted with a mixture of toluene (2.9 g) and EtOAc (2.9 g). The organic layers are combined and washed with fresh Rochelle's salt solution (2.6 g in 10.3 g water) and then with water (12.9 g). The resulting organic layer is dried over sodium sulfate (1.97 g), filtered, and concentrated in vacuo. The product is crystallized via a charge and concentration solvent exchange first to IPA (6.5 g) and then Heptane (7.7 g). The thick heptane slurry (-2.7 g) is stirred overnight and solids are collected by filtration. Vacuum drying affords 24d (550 mg) in an 85% yield.
Figure imgf000063_0001
[0150] The enone 24d (459 mg) and Johnson-Matthey 5% palladium on carbon (A503023-5, 101 mg) are charged to an appropriately sized multi neck reaction vessel. The vessel is purged with nitrogen and 3-picoline (2.2 g) is charged as the solvent. Stirring is started and the vessel is first degassed using nitrogen and then stirred under hydrogen at atmospheric pressure for 8 hours. At the end of the reaction, the catalyst is removed by filtration through 0.2 micron media, rinsing with ACN (1.4 ml). The filtrate and rinse are combined in a clean reaction vessel equipped with mechanical stirring, an internal temperature probe, and a nitrogen atmosphere. A solution of citric acid (3.7 g) in water (9.2 ml) is charged to the reaction vessel at or below 3O0C, and IPI-335589 is allowed to slowly crystallize from solution as the citrate salt at 20 and then O0C. The crystalline product is recovered by suction filtration and washed with water (3.7 ml). After drying, the citrate salt, 24e, is isolated as a hydrate (3-5 wt% water) in 89.5% yield (622 mg) with a β:α ratio approaching 90:1.
CBzCI, Na2CO3,
2-MeTHF/H2O
Figure imgf000063_0002
Figure imgf000063_0003
[0151] 24e (1.50 g) is charged to the appropriately sized reactor along with 2- methyltetrahydrofuran (7.7 g) and IM sodium carbonate (9.0 ml) A solution of benzyl chloroformate (454 mg) in 2-methyltetrahydrofuran (300 mg) is added via addition funnel and the reaction is ambient temperature for 1-2 hours. When the reaction is complete, the stirring is stopped, the layers are separated and the organic layer is washed twice with water (2 x 6 g). The organic layer is dried over of sodium sulfate (3 g), filtered and concentrated. Residual water is reduced further by concentration from fresh 2-methyltetrahydrofuran (6.5 g) and the material is transferred as solution in anhydrous 2-methyltetrahydrofuran to the next reaction.
Figure imgf000064_0001
[0152] Commercial 1 M K-Selectride in THF (1.20 g) is charged to a dry reaction vessel under a nitrogen atmosphere, diluted with anhydrous 2-methyltetrahydrofuran (2.10 g) and cooled to -650C. The solution of 24f (0.41 g) in 2-methyltetrahydrofuran (1.5 g), is then slowly added to the reaction vessel to control the internal temperature at -65±5°C. The reaction is stirred for 2 hours and warmed to -2O0C over approximately 1 hour and stirred for an additional hour. The reaction is monitored by HPLC and reactions that are incomplete are driven to completion with additional K-selectride. The reaction is quenched at low temperature with MeOH (0.33 g), then 3M NaOH (2.4 g) at -200C and 15% hydrogen peroxide in water (1.04 g) at or below 5°C, then stirring overnight at ambient temperatures. The layers are split and the organic layer is washed sequentially with IM aqueous NaOH (2 ml), 0.5 M aqueous Na2SO3 (2 ml), and water (2 ml) adjusted to a pH of 3 with HCl. The organic layer is dried over sodium sulfate (0.82 g), filtered and concentrated. The product 24g (0.457 g) is re-concentrated from DCM (0.9 g) and used in the next reaction.
Figure imgf000064_0002
24g 24h
[0153] 24g (1.36 g) is charged with anhydrous DCM (18.1 g) to an appropriately size reaction vessel, place under an inert atmosphere and cooled to -200C. Triethylamine (0.61 mg) is charged followed by the slow addition of methanesulfonyl chloride (373 mg) in anhydrous DCM (300 mg). The reaction is stirred for 1 hour at -200C. The reaction is monitored by HPLC. Incomplete reactions are driven to completion with additional methanesulfonyl chloride. When complete, the reaction is quenched with water (13.6 g) and allowed to warm. The layers are separated and the organic layer is washed with 2.5 wt% sodium bicarbonate (13.8 g) and then water (10.9 g). The organic layer is dried over of sodium sulfate (4 g), filtered, and concentrated. The product solution is solvent exchanged via charge and concentration to t-butyl methyl ether (10.9 ml) and then l,3-dimethyl-3,4,5,6-tetrahydro- 2(lH)-pyrimidinone (DMPU, 4.7 ml). The DMPU solution is used directly in the next reaction.
Figure imgf000065_0001
[0154] Sodium azide (0.74 g) is charged to an appropriately sized reaction vessel. The solution of 24h (1.46 g) in DMPU (5.9 g) is charged to the reaction vessel, rinsing with additional DMPU (1.9 g). The suspension is heated to 600C for 15 hours, maintaining a nitrogen sweep for the entire reaction. The reaction is cooled to ambient temperature and diluted with MTBE (11.7 g). The organic solution is washed 3 times with 2% saline (3 x 8 g), dried over sodium sulfate (4.4 g), filtered, and concentrated. The product is concentrated from THF (6.4 g) and used directly in the next reaction.
Figure imgf000065_0002
[0155] The crude 24i (1.34 g) is dissolved and transferred to a suitably sized reaction vessel with THF (12.6 g). Triphenylphosphine (0.70 g) and water (0.44 g) are charged and the reaction is heated to 55°C for 15-24 hours. When complete, the reaction is cooled to ambient temperature, dried with magnesium sulfate (1.4 g), filtered and concentrated. The solids are dissolved and concentrated from three portions of DCM (3 x 9 g) and purified by silica gel chromatography using DCM/MeOH/Et3N gradients to remove reagent based impurities. The pooled fractions are concentrated to dryness, dissolved in DCM (6.8 g) and concentrated to dryness again to afford an amorphous solid (1.12 g) which is used in the next reaction.
Figure imgf000066_0001
[0156] 24j (1.09 g) is dissolved and transferred to an appropriately sized reaction vessel with anhydrous DCM (15.8 g) and placed under a nitrogen atmosphere. The solution is cooled to 00C. N,N-diisopropylethylamine (357 mg) and neat methanesulfonyl chloride (0.165 ml) are charged sequentially while maintaining temperature between below 5 0C. The reaction is monitored by HPLC. Incomplete reactions are driven to completion with additional methanesulfonyl chloride. The reaction is quenched with 0.4 M aqueous sodium bicarbonate (11.4 g) and warmed to ambient temperature. The layers are separated and the aqueous phase is back extracted with DCM (5.8 g). The combined organic layers are dried over magnesium sulfate (0.55 g), filtered and concentrated. The product 24k is dissolved and striped from 2- propanol (4.0 g) to remove residual DCM and used directly in the next reaction.
Figure imgf000066_0002
[0157] Aldrich Degussa type ElOl NE/W 10% Pd/C (249 mg) is charged to an appropriately sized reaction vessel and placed under a nitrogen atmosphere. A 2-propanol (9.8 g) solution of 24k (1.24 g) is charged to the reaction vessel. The system is degassed and placed under a nitrogen atmosphere, and the process is repeated with hydrogen. The reaction is stirred under a 1 atm of hydrogen at ambient temperature for 8 hours. An inert atmosphere is returned to the vessel and a second charge of catalyst (125 mg) slurried in 2-propanol (0.5 g) is added to the reaction. The reaction mixture is degassed and placed under a nitrogen atmosphere, and the process is repeated with hydrogen. The reaction is stirred under 1 atm of hydrogen for another 15 hours at ambient temperature. The reaction is monitored by HPLC. Incomplete reactions are treated with additional catalyst and hydrogen. When complete, the reaction is filtered, treated with steam activated carbon (200 mg), and filtered again. The solution is dried by partial concentration transferred to a reaction vessel and diluted with anhydrous 2-propanol to 0.09 M based on the theoretical yield. A 1.25 M HCl solution in 2- propanol (1.64 g) is charged over 20 minutes. The hydrochloride salt crystallizes slowly with gentle stirring and is isolated by filtration. The crystals are washed with 2-propanol (2.5 g) and vacuum dried to afford Compound 42 (916 mg, 80% yield) as a 1:1 IPA solvate.
Example 25
Figure imgf000067_0001
47
Figure imgf000067_0002
42 48
[0158] A round-bottom flask was charged with the amine 42 (1.1 g, 2.1 mmol, 1 equiv.), dry tetrahydrofuran (10 ml) and pyridine (880 uL, 10.9 mmol, 5 equiv.). The cooled (00C) mixture was treated with benzoylperoxide (1.6 g, 6.5 mmol, 3 equiv.). The mixture was stirred for 2 hours at 00C then overnight at 25°C. Reaction mixture diluted with MTBE and washed with a mixture of saturated aqueous NaHCCb with 1 N NaOH until the layer split. The organic layer was collected and the aqueous was re-extracted once with MTBE. Combined organic layers were washed with brine, dry over Na2SO4, filtered and concentrated to dryness. The crude oil was dissolved in 5 mL of CH2Cl2, loaded onto SiO2 (40 g) column and eluted from hexanes/EtOAc (10% to 50%) to give the benzoyl derivative 48 (380 mg) ([M+H] = 625.4 m/z). Step B
Figure imgf000068_0001
48 47
[0159] A round-bottom flask was charged with 48 (374 mg, 0.6 mmol, 1 equiv.) and MeOH (5 mL). The solution was treated at 25°C in presence of 2 N KOH (0.3 mL, 0.6 mmol, 1 equiv.). The mixture was stirred for 3h. The solvent was removed under vacuum. MTBE was added to the residue, which was neutralized with IN HCl. The layers were cut and the aqueous layer was extracted with two portions of CH2Cl2. Combined organic layers were dried over Na2SO4, filtered, and concentrated to dryness. The crude material (380 mg) was dissolved with CH2Cl2, loaded onto a SiO2 column (12 g) and eluted with hexanes/EtOAc (0% to 100%) to give the hydroxylamine 47. The material was lyophilized from t-BuOH/7% H2O to give 213 mg of 47 as a white powder ([M+H] = 521.4 m/z).
Figure imgf000068_0002
50
Figure imgf000069_0001
51
[0160] A heat-gun dried flask was charged with dry CH2CI2 (5 mL) and benzyl alcohol (785 uL, 7.58 mmol, 1.3 equiv.). The cooled (00C) solution was treated with chlorosulfonyl isocyanate (506 uL, 5.83 mmol, 1 equiv.). Then, DMAP (1.4 g, 11.6 mmol, 2 equiv.) was added and the mixture was stirred for 1 h at 25°C. After complete dissolution of DMAP, the reaction was clear for a short period. Then, a white fluffy precipitate formed. The mixture was diluted with CH2CI2 (30 mL) and washed with three portions (30 mL each) of water. The organic layer was dried over Na2SO4, filtered, and evaporated to dryness. The desired white solid 51 was taken to the next step without purification. Step B
Figure imgf000069_0002
52 53
[0161] A round-bottom flask was charged with 52 (30 mg, 0.053 mmol, 1 equiv.) and
51 (18 mg, 0.053 mmol, 1 equiv.). Both reagents were dissolved in CH2Cl2 (2 mL) and the solution was stirred at 25°C. The crude material was loaded onto a SiO2 column (4 g) and eluted with hexanes/EtOAc (0% to 50%) to give 16 mg of the sulfamoylated derivative 53 ([M+Na] = 796.4 m/z).
Figure imgf000070_0001
53 50
[0162] A round-bottom flask was charged with 53 (16 mg, 0.021 mmol, 1 equiv.) and 11 mg of 10% Pd/C (wet,Aldrich Degussa type ElOl). The material was suspended in 2- propanol (3 mL). The flask was sealed and purged three times with hydrogen and left overnight under 1 atm of hydrogen. The slurry was filtered through 0.2 micron Acrodisc, washed with 2-propanol, and the solvent was removed under vacuum. The residue was purification by SiO2 column (1 g) eluting with CH2Cl2/Me0H (5% to 10%). The major product was lyophilized from t-BuOH/7% H2O to give 9 mg of sulfamide 50 ([M+H] = 506.4 m/z).
Example 27
Figure imgf000070_0002
55
Figure imgf000070_0003
56 [0163] A round-bottom flask was charged with cyclopamine 4-en-3-one (3.5 g, 8.5 mmol, 1 equiv.) and pyridine (70 mL). The reactor was charged with Pd/C (10% Pd, 500 mg). The reaction was placed under 1 atmosphere of hydrogen. After 3.5 hrs, LCMS showed complete consumption of starting material. The catalyst was filtered off on an Acrodisk 0.2 micron filter and washed with toluene. The solvent was removed by azeotropic removal with toluene (2 x 10 mL). The desired material 56, 3.5 g ([M+H] = 412.5 m/z) was used as it for the next step. Step B
Figure imgf000071_0001
56 57
[0164] A round-bottom flask was charged with 56 (1.2 g, 2.8 mmol, 1 equiv.), CH2Cl2 (10 mL) and triethylamine (1.9 mL, 14.2 mmol, 5 equiv.). The cooled (00C) solution was treated with CBz-Cl (440 uL, 2.8 mmol, 1 equiv.). After 1 hr, LCMS showed complete consumption of starting material. The mixture was diluted with water. The layers were cut and the organic layer was washed twice with water. The organic layer was dried over sodium sulfate, filtered, and concentrated to dryness. The product was purified by column chromatography (SiO2, 40 g) eluting with hexane/EtOAc (0 to 20%) to give 57 (891 mg) ([M+Na] = 468.4 m/z).
Figure imgf000072_0001
57 58
[0165] In a round-bottom flask, the ketone 57 was azeotroped a couple times with CH2CI2 and dried under vacuum for 1 h. Under nitrogen, the ketone 2 (693 mg, 1.27 mmol, 1 equiv.) was dissolved in anhydrous THF (20 mL) and the solution was cooled to -78C. A I M solution of K-selectride in THF (1.9 mL, 1.9 mmol, 1.5 equiv.) was added dropwise. After 1 h, the reaction was complete by TLC. The reaction was quenched by addition of 2.6 mL of 5 N NaOH followed by slow addition of 2.6 mL of 30% wt H2O2. The resulting mixture was allowed to stir overnight. The mixture was partitioned between water and EtOAc. The aqueous layer was back extracted with EtOAc. The combined organic were washed first with water (buffered with a small portion of ammonium chloride) then with brine. The organic were dried, filtered, and concentrated to a crude foam (840 mg) The crude material was dissolved in CH2Cl2, loaded on a SiO2 column (4Og) and eluted with hexanes/EtOAc (0 to 50%) to give 58 (565 mg). Step D
Figure imgf000072_0002
58 59
[0166] In a round-bottom flask under nitrogen, the alcohol 58 (530 mg, 0.98 mmol, 1 equiv.) was dissolved in 5 mL of anhydrous CH2CI2 and triethylamine (800 uL, 5.81 mmol, 6 equiv.). The reaction mixture was cooled to 00C and Ms-Cl (112 uL, 1.45 mmol, 1.5 equiv) was added dropwise. The mixture was stirred at 00C for 30 min. TLC (hexane: EtOAC, 7:3) showed ~ 70% conversion. 70 uL of triethylamine (70 uL, 0.5 equiv.) and Ms-Cl (10 uL, 0.1 equiv) were charged to the reaction vessel. After 90 min, a solution of saturated bicarbonate was charged and the residue was extracted with CH2CI2. The organic layer was washed with water, dried and concentrated to a off-white foam. The material was dissolved in CH2Cl2 and purified with SiO2 (40 g) eluting with hexanes/EtOAc (0% to 50%) to give 59 (430 mg). Step E
Figure imgf000073_0001
59 60
[0167] In a round-bottom flask, the mesylate 59 (420 mg, 0.67 mmol, 1 equiv.) was dissolved in 2 mL of DMPU. The solution was treated with sodium azide (218 mg, 3.4 mmol, 5 equiv.) at 6O0C for 5 h. The mixture was cooled to 25°C, then poured into ice-water to generate a white solid. The compound was extracted with MTBE (3 times). The combined organic layers were washed with water (2X), then brine. The organic layers were dried over Na2SO4, filtered, and concentrated to a white foam (342 mg). The desired material 60 was used as is for the next step. Step F
Figure imgf000074_0001
60 61
[0168] In a round-bottom flask equipped with a condenser, the azide 60 (336 mg, 0.58 mmol, 1 equiv.) was dissolved in 7 mL of THF and 140 uL of water and treated with triphenylphosphine (462 mg, 1.76 mmol, 3 equiv.). The mixture was heated to 700C overnight. TLC (hexane/EtOAc, 7:3) confirmed the reaction was complete. The reaction was concentrated to dryness. The crude material was dissolved in CH2Cl2, loaded onto 12 g of SiO2 and eluted with CH2Cl2MeOH (0 to 20%) to give the amine 61 (254 mg). Step G
Figure imgf000074_0002
61 62
[0169] In a round-bottom flask under nitrogen, the amine 61 (248 mg, 0.45 mmol, 1 equiv.) was dissolved in 7 mL of anhydrous CH2Cl2 and N,N-diisopropylethylamine (237 uL, 0.91 mmol, 2 equiv.). The reaction mixture was cooled to 00C and Ms-Cl (70 uL, 1.45 mmol, 1.5 equiv) was added dropwise. The mixture was stirred at 00C for 2 h. TLC (hexane/EtOAc, 7:3) showed a little amount of amine. The mixture was charged with 10 uL of Ms-Cl (0.2 equiv.), and warmed to 25°C for Ih. The reaction mixture was diluted with CH2CI2 then a saturated solution of NaHCCb. The layers were cut. The aqueous layer was extracted with one portion of CH2CI2. The combined organic layers were washed with water, dried over Na2SO4, filtered and concentrated to dryness. The crude (326 mg) was added to a SiO2 column (12 g) and was eluted with hexanes/EtOAc (0 to 50%) to give the sulfonamide 62 (256 mg). Step H
Figure imgf000075_0001
62 55
[0170] A round-bottom flask was charged with the sulfonamide 62 (250 mg, 0.4 mmol, 1 equiv.) and 50 mg of 10% Pd/C (wet,Aldrich Degussa type ElOl lot 0833 IKC). The material was suspended in EtOAc (5 mL). The flask was sealed and purged three times with hydrogen and stirred under 1 atm of hydrogen. After 3 h some conversion was observed, but a lot of starting material remained. The slurry was filtered through 0.2 micron Acrodisc, washed with 2-propanol. The filtrate solution was re-subjected to the reaction condition by adding 54 mg of catalyst. The reaction was completed after 3 h. The slurry was filtered through 0.2 micron Acrodisc, washed with 2-propanol, and the solvent was concentrated to dryness. The crude material (200 mg) was loaded onto a SiO2 column (12 g) and the compound was eluted using a gradient CH2Cl2/Me0H (0 to 10%) to give the free amine. The material was lyophilized from t-BuOH/7% H2O to give 175 mg of 55 as a white powder ([M+H] = 491.3 m/z).
Example 28: Inhibition of the Hedgehog pathway in cell culture
[0171] Hedgehog pathway specific cancer cell killing effects may be ascertained using the following assay. C3H10T1/2 cells differentiate into osteoblasts when contacted with the sonic hedgehog peptide (Shh-N). Upon differentiation; these osteoblasts produce high levels of alkaline phosphatase (AP) which can be measured in an enzymatic assay (Nakamura et al., 1997 BBRC 237: 465). Compounds that block the differentiation of C3H10T1/2 into osteoblasts (a Shh dependent event) can therefore be identified by a reduction in AP production (van der Horst et al., 2003 Bone 33: 899). The assay details are described below. The results approximate (EC50 for inhibition) of the differentiation assay is shown below in Table 1.
Assay Protocol
Cell Culture
[0172] Mouse embryonic mesoderm fibroblasts C3H10T1/2 cells (obtained from ATCC) were cultured in Basal MEM Media (Gibco/Invitrogen) supplemented with 10% heat inactivated FBS (Hyclone), 50 units/ml penicillin and 50ug/ml streptomycin (Gibco/Invitrogen) at 37C with 5% CO2 in air atmosphere.
Alkaline Phosphatase Assay
[0173] C3H10T1/2 cells were plated in 96 wells with a density of 8xlO3 cells/well. Cells were grown to confluence (72hrs). After sonic Hedgehog (250ng/ml), and/or compound treatment, the cells were lysed in 110 μL of lysis buffer (50 mM Tris pH 7.4, 0.1% TritonXlOO), plates were sonicated and lysates spun through 0.2 μm PVDF plates (Corning). 40 μL of lysates was assayed for AP activity in alkaline buffer solution (Sigma) containing lmg/ml p-Nitrophenyl Phosphate. After incubating for 30 min at 37 0C, the plates were read on an Envision plate reader at 405 nm. Total protein was quantified with a BCA protein assay kit from Pierce according to manufacturer's instructions. AP activity was normalized against total protein. Note that "A" indicates that the IC50 is less than 20 nM, "B" indicates that the IC50 is 20-100 nM, "C" indicates that the IC50 is > 100 nM.
Table 1 -- Approximate EC50 for Inhibition Compound Differentiation Assay EC50
1 A
7 C
8 C
9 C
10 C 13 A
20 A
21 B
22 A
23 A
24 A 27 B 29 B 31 B 33 C 35 A 37 A
39 B
40 A 42 A 55 A
Examples 29: Pancreatic Cancer Model
[0174] The activity of Compound 42 was tested in a human pancreatic model: BXPC-3 cells were implanted subcutaneously into the flanks of the right legs of mice. On day 42 post-tumor implant, the mice were randomized into two groups to receive either Vehicle (30%HPBCD) or Compound 42. Compound 42 was dosed at 40mg/kg/day. After receiving 25 daily doses, Compound 42 statistically reduced tumor volume growth by 40% when compared to the vehicle control (p=0.0309). At the end of the study, the tumors were harvested 4 hours post the last dose to evaluate an on target response by q- RT- PCR analysis of the HH pathway genes. Analysis of human GIi-I resulted in no modulation. Analysis of murine GIi-I mRNA levels resulted in a robust down-regulation in the Compound treated group, when compared to the Vehicle treated group.
Example 30: Medulloblastoma Model
[0175] The activity of Compound 42 was also evaluated in a transgenic mouse model of medulloblastoma. Mice that are heterozygous for loss of function mutations in the tumor suppressors Patchedl (Ptchl) and Hypermethylated in Cancer (Hicl) develop spontaneous medulloblastoma. Similar to human medulloblastoma, these tumors demonstrate complete promoter hypermethylation of the remaining Hicl allele, as well as loss of expression of the wild type Ptchl allele. When passaged as subcutaneous allografts, these tumors grow aggressively and are Hedgehog pathway-dependent. This model was employed to evaluate the efficacy of orally administered Compound, and to correlate activity with drug exposure in plasma and tumors. Oral administration (PO) of a single dose of Compound 42 led to dose-dependent down-regulation of the HH pathway in subcutaneously implanted tumors, as measured by decreased GIi-I mRNA expression 8 hours post dose administration.
[0176] Daily (QD) administration of the Compound PO led to a dose dependent inhibition of tumor growth, with frank tumor regression seen at higher doses. The approximate effective daily oral dose for 50% inhibition of tumor growth (ED50) is 4mg/kg. When animals were treated QD for 21 days, long term survival was observed following cessation of treatment (>60 days), with little to no tumor re-growth. Example 31 : Lung Cancer Model
[0177] To test the activity of Compound 42 in a human SCLC tumor model, LX22 cells were implanted subcutaneously into the flank of the right leg. LX22 is primary xenograft model of SCLC derived from chemo -naive patients, which has been maintained by mouse to mouse passaging. This tumor responds to etoposide/carboplatin chemotherapy in way that closely resembles a clinical setting. LX22 regresses during chemotherapy treatment, goes through a period of remission, and then begins to recur. In the LX22 model, Compound single agent activity and its ability to modulate the chemoresistant recurrence was tested. On day 32 post tumor implant, mice were randomized into three dosing groups to receive Vehicle (30% HBPCD), Compound, or the chemotherapy combination of etoposide and carboplatin (E/P). Compound 42 was administered at a dose of 40mg/kg/day, and after 16 consecutive doses there was no measurable difference between the treated and vehicle groups. Etoposide was administered i.v at 12mg/kg on days 34, 35, 36, and 48, while Carboplatin was administered i.v. at 60mg/kg on days 34, 41, and 48, post tumor implant. On day 50, the E/P treated mice were further randomized to receive either Vehicle (30%HPBCD) or Compound follow up treatment. The Compound was administered at the oral multi-dose MTD of 40mg/kg/day, and after 35 consecutive doses there was a substantial delay in tumor recurrence in the treated group, compared to the vehicle group (p=0.0101). Incorporation by Reference
[0178] All of the U.S. patents and U.S. published patent applications cited herein are hereby incorporated by reference. Equivalents
[0179] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

1. A compound represented by the following structure:
Figure imgf000080_0001
or a pharmaceutically acceptable salt thereof; wherein R1 is H, alkyl, -OR, amino, sulfonamido, sulfamido, -OC(O)R5, - N(R5)C(O)R5, or a sugar;
R2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, nitrile, or heterocycloalkyl; or R1 and R2 taken together form =0, =S, =N(0R), =N(R), =N(NR2), or =C(R)2;
R3 is H, alkyl, alkenyl, or alkynyl;
R4 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR5, -C(O)R5, -CO2R5, -SO2R5, -C(O)N(R5)(R5), -[C(R)2]q-R5,
-[(W)-N(R)C(0)]qR5, -[(W)-C(0)]qR5, -[(W)-C(0)0]qR5, -[(W)-0C(0)]qR5,
-[(W)-SO2]qR5, -[(W)-N(R5)SO2]qR5, -[(W)-C(O)N(R5)]qR5, -[(W)-0]qR5,
-[(W)-N(R)]qR5, -W-NR5 S +X" or -[(W)-S]qR5; wherein each W is, independently, a diradical; each q is independently for each occurrence 1,
2, 3, 4, 5, or 6;
X" is a halide; each R5 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl or -[C(R)2]P-R6; wherein p is 0-6; or any two occurrences of R5 on the same substituent can be taken together to form a 4-8 membered optionally substituted ring which contains 0-3 heteroatoms selected from N, O, S, and P; each R6 is independently hydroxyl, -N(R)COR, -N(R)C(O)OR, -N(R)SO2(R),
-C(O)N(R)2, -OC(O)N(R)(R), -SO2N(R)(R), -N(R)(R), -COOR, -C(O)N(OH)(R),
-OS(O)2OR, -S(O)2OR, -OP(O)(OR)(OR), -NP(O)(OR)(OR), or -P(O)(OR)(OR); provided that when R2, R3, and R4 are H; R1 is not hydroxyl or a sugar; further provided that when R4 is hydroxyl, then R1 is not a sugar or hydroxyl; further provided that when R4 is hydroxyl, then R1 and R2 together are not C=O. The compound of claim 1, wherein R1 is H, hydroxyl, alkoxyl, aryloxy, or amino or wherein R1 and R2 taken together along with the carbon to which they are bonded, form =O, =N(0R), or =S.
3. The compound of claim 1 , wherein R3 is H.
4. The compound of claiml, wherein R4 is H, alkyl, hydroxyl, aralkyl, -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-N(R)SO2]qR5, -[(W)-C(0)N(R)]qR5, -[(W)-0]qR5, -[(W)-C(0)]qR5, or -[(W)-C(0)0]qR5.
5. The compound of claim 1 , wherein R1 is H or -OR, R2 is H or alkyl, and R4 is H.
6. The compound of claim 1 , wherein R3 is H or alkyl and R2 is H or alkyl.
7. The compound of claim 1 , wherein R4 is H, alkyl, aralkyl, -[(W)-N(R)C(0)]qR5, -[(W)-N(R)SO2]qR5, -[(W)-C(0)N(R)]qR5, -[(W)-0]qR5, -[(W)-C(0)]qR5, or -[(W)-C(0)0]qR5 and R3 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, or aralkyl.
8. The compound of claim 1 , wherein R4 is H, alkyl, aralkyl, -[(W)-C(O)N(R)]qR5,or
-[(W)-N(R)C(0)]qR5.
9. The compound of claim 1 , wherein R > 11 : is, sulfonamide
10. The compound of claim 1 , wherein said compound is isolated.
11. A compound selected from the group consisting of:
Figure imgf000081_0001
Figure imgf000082_0001
Figure imgf000083_0001
Figure imgf000084_0001
12. An isolated compound selected from the group consisting of:
Figure imgf000084_0002
13. A compound represented by the following structure:
Figure imgf000084_0003
or a pharmaceutically acceptable salt thereof; wherein R1 is H, alkyl, -OR, amino, sulfonamido, sulfamido, -OC(O)R5, - N(R5)C(O)R5, or a sugar;
R2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, nitrile, or heterocycloalkyl; or R1 and R2 taken together form =0, =S, =N(0R), =N(R)-, =N(NR2), =C(R)2; R3 is H, alkyl, alkenyl, or alkynyl;
R4 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR5, -C(O)R5, -CO2R5, -SO2R5, -C(O)N(R5)(R5), -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-C(0)]qR5, -[(W)-C(0)0]qR5, -[(W)-0C(0)]qR5, -[(W)-SO2]qR5, -[(W)-N(R5)SO2]qR5, -[(W)-C(O)N(R5)]qR5, -[(W)-0]qR5, -[(W)-N(R)]qR5, -W-NR5S+X", or -[(W)-S]qR5; wherein each W is, independently, a diradical; each q is, independently, 1, 2, 3, 4, 5, or 6; X" is a halide; each R5 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl or -[C(R)2]P-R ; wherein p is 0-6; or any two occurrences of R5 on the same substituent can be taken together to form a 4-8 membered optionally substituted ring which contains 0-3 heteroatoms selected from N, O, S, and P; each R6 is, independently, hydroxyl, -N(R)COR, -N(R)C(O)OR, -N(R)SO2(R), -C(O)N(R)2, -OC(O)N(R)(R), -SO2N(R)(R), -N(R)(R), -COOR, -C(O)N(OH)(R), -OS(O)2OR, -S(O)2OR, -OP(O)(OR)(OR), -NP(O)(OR)(OR), or -P(O)(OR)(OR); each of R7 and R7 is H; or R7 and R7 taken together form =0;
R and R taken together form a bond; each R is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl or aralkyl; and provided that when R3, R4, R8, R9 are H and , R7 and R7 taken together form =0; R1 can not be hydroxyl and R2 can not be H; provided that when R3, R4, R8, R9 are H and , R7 and R7 taken together form =0; R1 can not be acetate and R2 can not be H; provided that when R3, R4, R8, R9 are H and , R7 is H2; R1 and R2 taken together can not be =0; and provided that when R3, R4, R8, R9 are H and , R7 and R7 are H; R1 and R2 can not be H.
14. The compound of claim 13, wherein said compound is epimerically pure.
15. The compound of claim 13, wherein said compound is isolated.
16. The compound of claim 13, wherein R4 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR5, -[C(R)2]q-R5, -[(W)-N(R)C(0)]qR5, -[(W)-C(0)]qR5, -[(W)-C(0)0]qR5, -[(W)-0C(0)]qR5, -[(W)-SO2]qR5, -[(W)-N(R5)SO2]qR5, -[(W)-C(O)N(R5)]qR5, -[(W)-O]qR5, -[(W)-N(R)]qR5, or -[(W)-S]qR5.
17. The compound of claim 13, wherein each of R7 and R7 is H.
18. The compound of claim 13, wherein R1 and R2 taken together form =0 and each of R7 and R7 is H.
19. A compound selected from the group consisting of:
Figure imgf000086_0001
or a pharmaceutically acceptable salt thereof
20. A pharmaceutical composition comprising a compound of claim 1, and at least one pharmaceutically acceptable excipient.
21. A process for preparing a compound of formula 136:
Figure imgf000086_0002
136 wherein Y is CR7R8;
R1 is H, alkyl, amino, hydroxyl, carboxyl, carbamoyl, alkoxy, hydroxyl, sugar or a protected hydroxyl group;
R2 is H, alkyl, alkenyl, alkynyl, nitrile, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
R1 and R2 taken together form =0, =S, =N(0R9), =N(R9), =C(R9)2, or =N(N(R9)2); each of R3, R4, and R5 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
R3 and R4 or R4 and R5 taken together form a bond;
R6 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR9, -C(O)R9, -CO2R9, -SO2R9, -C(O)N(R9)(R9), -[C(R9)2]qR9,
-[(W)-N(R9)C(O)]qR9, -[(W)-C(0)]qR9, -[(W)-C(0)0]qR9, -[(W)-0C(0)]qR9,
-[(W)-SO2]qR9, -[(W)-N(R9)SO2]qR9, -[(W)-C(O)N(R9)]qR9, -[(W)-0]qR9,
-[(W)-N(R9)]qR9, -[(W)-S]qR9, or a nitrogen protecting group; wherein each W independently for each occurrence is a diradical; each q is independently 1, 2, 3, 4, 5, or 6; each of R7 and R8 is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester; each R9 is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; said process comprising the steps of: contacting a compound of formula 136a with a haloalkylzinc phosphate cyclopropanating agent;
Figure imgf000087_0001
136a wherein
R1, R2, R3, R4, R5, R6 are as defined above; to form said compound of formula 136.
22. The process of claim 21, wherein R7 and R8 are both H.
23. The process of claim 21, wherein R1 is a protected hydroxyl.
24. The process of claim 21, wherein R6 is a nitrogen protecting group.
25. The process of claim 21 , where said haloalkylzinc phosphate cyclopropanating agent is formed by combining a phosphoric acid of formula 141a, a dialkylzinc, and a dihaloalkylane of formula 141b:
Figure imgf000088_0001
141a 141b wherein each of X and X' is independently chloride, bromide, or iodide; each of R7 and R8 is independently H, alkyl, halide, amido, or ester; each of R10 and R11 is independently alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R10 and R11 taken together have the formula 141c, 141d, or 141e;
Figure imgf000088_0002
141c 141d 141e wherein m independently for each occurrence is 0, 1, 2, 3, or 4; n independently for each occurrence is 0,1, or 2; and each of R12, R13, R14, R15, R16, R17 and R18 is, independently, alkyl, aryl, aralkyl, or halide.
26. The process of claim 25, wherein R10 and R11 are each 2,6-dimethylphenyl.
27. A process for preparing a compound of formula 137:
Figure imgf000089_0001
137 wherein
Y is CR7R8;
R1 is H, alkyl, amino, hydroxyl, carboxyl, carbamoyl, alkoxy, hydroxyl, sugar or a protected hydroxyl group;
R2 is H, alkyl, alkenyl, alkynyl, nitrile, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
R1 and R2 taken together form =0, =S, =N(0R9), =N(R9), =C(R9)2, or =N(N(R9)2); each of R3, R4, and R is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
R3 and R4 or R4 and R taken together form a bond;
R6 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, heteroaralkyl, haloalkyl, -OR9, -C(O)R9, -CO2R9, -SO2R9, -C(O)N(R9)(R9), -[C(R9)2]qR9,
-[(W)-N(R9)C(O)]qR9, -[(W)-C(0)]qR9, -[(W)-C(0)0]qR9, -[(W)-0C(0)]qR9,
-[(W)-SO2]qR9, -[(W)-N(R9)SO2]qR9, -[(W)-C(O)N(R9)]qR9, -[(W)-0]qR9,
-[(W)-N(R9)]qR9, -[(W)-S]qR9, or a nitrogen protecting group; wherein each W independently for each occurrence is a diradical alkylene having 1-6 carbon atoms; each q is independently 1, 2, 3, 4, 5, or 6; each of R7 and R8 is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester; each R9 is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl,aralkyl, heteroaryl, or heteroaralkyl; said process comprising the steps of: contacting a compound of formula 137a with a haloalkylzinc phosphate cyclopropanating agent;
Figure imgf000090_0001
137a wherein
R1, R2, R3, R4, R5, R6 are as defined above; to form a compound with formula 137b
Figure imgf000090_0002
137b wherein
R1, R2, R3, R4, R5, R6 and Y are as defined above; and contacting said compound of formula 137b with an acid to give said compound of formula 137.
28. A process for preparing a compound of formula 142:
Figure imgf000090_0003
142 comprising the steps of: contacting a compound of formula 142a with a cyclopropanating agent to form a compound formula 142b; and
Figure imgf000091_0001
142a
Figure imgf000091_0002
142b combining said compound of formula 142b with an acid to give said compound of formula 142; wherein
Y is CR7R8;
R1 is a protected hydroxy 1 group;
R2 is H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; each of R3, R4, and R is, independently, H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl; or
R3 and R4, or R4 and R taken together form a bond;
R6 is a nitrogen protecting group; each of R7 and R8 is, independently, H, alkyl, alkenyl, aryl, nitrile, amido, halide, or ester; and each R9 is independently H, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, heterocycloalkyl, aralkyl, heteroaryl, or heteroaralkyl.
29. The process of claim 28, wherein R and R are both H.
30. The process of claim 28, wherein said protected hydroxyl group is an ester or a carbonate.
31. The process of claim 28, wherein said nitrogen protecting group is a carbamate.
32. The process of claim 28, wherein said nitrogen protecting group is an amide.
33. The process of claim 28, wherein R2 and R3 are H and R4 and R5 taken together form a bond.
34. The process of claim 28, wherein said cyclopropanating agent is generated from a dihaloalkane and a metal species.
35. The process of claim 34, wherein said metal species is dialkyl zinc or a zinc copper couple.
36. The process of claim 28, wherein said cyclopropanating agent is generated from a dihaloalkane species and a dialkyl zinc species, and a phosphoric acid species or a salt thereof.
37. The process of claim 28, wherein said phosphoric acid species has a structure of formula 151:
Figure imgf000092_0001
151 or a salt thereof; wherein each of R10 and R11 is independently alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R10 and R11 taken together have the formula 151a, 151b, or 151c;
Figure imgf000092_0002
wherein m independently for each occurrence is 0, 1, 2, 3, or 4; n independently for each occurrence is 0,1, or 2; each of R12, R13, R14, R15, R16, R17 and R18 is, independently, alkyl, aryl, aralkyl, or halide.
38. The process of claim 28, wherein said acid is acetic acid, trifluoromethanesulfonic acid, phosphoric acid, methanesulfonic acid or HCl.
39. The process of claim 28, wherein said acid is BF3, zinc chloride, zinc methanesulfonate, or a zinc salt.
40. A process for preparing a compound of formula 156:
Figure imgf000093_0001
156 comprising the steps of: contacting a compound of formula 156a with a cyclopropanating agent to form a compound formula 156b; and
Figure imgf000093_0002
156b combining said compound of formula 156b with an acid to give said compound of formula 156; wherein
R1 is an oxygen protecting group selected from the group consisting of formate, acetate, chloroacetate, dichloroacetate, trichloroacetate, pivaloate, benzoates, alkyl carbonate, alkenyl carbonate, aryl carbonates, aralkyl carbonate, 2,2,2-trichloroethyl carbonate, alkoxymethyl ether, aralkoxymethyl ether, alkylthiomethyl ether, aralkylthio ether, arylthio ether, trialkylsilyl ether, alkylarylsilyl ether, benzyl ether, arylmethyl ether, allyl ether; and
R is a nitrogen protecting group selected from the group consisted of formyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, phenyl acetyl, benzoyl, alkyl carbamates, aralkyl carbamates, aryl carbamates, allyl, aralkyl, triarylmethyl, alkoxymethyl, aralkoxymethyl, N-2-cyanoethyl, diary lphosphinamides, dialkylphosphinamidates, diarylphosphinamidates, and trialkylsilyl.
41. The process of claim 40, where said cyclopropanating agent is formed by combining a phosphoric acid of formula 158a, a dialkylzinc, and a dihaloalkylane of formula 157b:
Figure imgf000094_0001
158a 158b wherein each of X and X' is, independently, chloride, bromide, or iodide; each of R7 and R8 is, independently, H, alkyl, halide, amido, or ester; each of R10 and R11 is, independently, alkyl, alkenyl, aralkyl, aryl, heteroaryl, heteroaralkyl; or R10 and R11 taken together have the formula 158c, 158d, or 158e;
Figure imgf000094_0002
wherein m independently for each occurrence is 0, 1, 2, 3, or 4; n independently for each occurrence is 0,1, or 2; each of R12, R13, R14, R15, R16, R17 and R18 is, independently, alkyl, aryl, aralkyl, or halide.
42. The process of claim 41, wherein said oxygen protecting group is alkyl carbonate, aralkyl carbonate, benzoate, pivaloate, or formate.
43. The process of claim 41, wherein said nitrogen protecting group is benzoyl, trichloroacetyl, trifluoroacetyl, formyl, alkyl carbamates, aralkyl carbamates, or aryl carbamates.
44. The process of claim 41, wherein said oxygen protecting group is benzylcarbonate.
45. The process of claim 41, wherein said nitrogen protecting group is benzylcarbamate.
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