diverted total synthesis in medicinal chemistry … total synthesis in medicinal chemistry research...

Diverted Total Synthesis inMedicinal Chemistry Research

Luke ZuccarelloDecember 14, 2005

Natural Products in Drug Therapy• About 50% of drugs in clinical use today are natural

products, or chemically modified natural products• Sources for natural product-derived drugs: (a) directly

from plant/animal, (b) genetic engineering, (c) semi-synthesis (d) total synthesis

• Pharmaceutical research involving natural products wasstagnant/declining in 1990s, but increasing again in thecurrent decade

Koehn, F. E.; Carter, G. T. Nat. Rev. Drug Disc.2005, 4, 206.

Why the Decline Natural Products Researchin the Pharmaceutical Industry?

• Advent of high-throughput screening (HTS) allows more compoundsto be assessed for hits

• Natural products are typically extracted as mixtures (10-100s) ofcompounds with largely varying concentrations, which can (a) makeidentifying actual active compound more difficult; (b) add more workin additional purification; (b) give poor results with catalysis/bindingassays

• Combinatorial chemistry/synthetic libraries are better suited for HTSthan natural product extract libraries, leading to an industrial trendtoward purely synthetic libraries

• Major decline in “big pharma” research on infectious diseasetherapy

Koehn, F. E.; Carter, G. T. Nat. Rev. Drug Disc. 2005, 4, 206.

Problems with Combinatorial Libraries inDrug Screening

• Libraries designed to maximize number of compoundsscreened (106) may yield no hits due to lack ofbiochemically relevant structure

• Compounds that are hits are often unselective in theirbinding/activity

• Overall, R&D expectations have not been realized


Advantages of Natural Product Libraries inDrug Screening

• Recent advances in purification and analysis technology allows for naturalproduct library HTS

• Natural products have been selected through evolution to interact withmacromolecules (eg proteins)

• This includes natural selection of 3D structures and pharmacophores• Many natural products are “priveleged structures,” allowing them to interact

with multiple biological targets in various types of organisms• This is reinforced by research in the last 5-10 years which shows that the

protein fold space found in nature is smaller than previously predicted• At the same time, natural products are typically specific in their ability to

modulate protein-protein interactions (signal transduction, immuneresponse, mitosis, apoptosis)

• Natural products typically do not violate Lapinski’s “Rule of Five”

Koehn, F. E.; Carter, G. T. Nat. Rev. Drug Disc. 2005, 4, 206.Zhang, C.; DeLisi, C. J. Mol. Biol. 1998, 284, 1301.

Types of Natural Product DerivedTherapeutics

1) Unaltered natural product as a drug



2) Semi-synthetic analog: chemical manipulation(typically functional group interconversion) of a naturalproduct

Example: exchanging a sugar on a natural product

Possible disadvantages: supply of natural product,limitations to available analogues due to nativefunctionality

Paterson, I.; Anderson, E. Science 2005, 310, 451.

Njardarson, J. T. ; Gaul, C.; Shan, D.; Huang, X.-Y.; Danishefsky, S. J. J. Am. Chem. Soc. 2004, 126, 1038..


3) Analogs from diverted total synthesis

Bryostatin: Potent Anti-cancer NaturalProduct

•Macrocyclic lactones from the marine invertebrate bugula neritina, first isolated in 1968; fully characterized in 1982•Bryostatins consist of at least 20 members, which vary at R1 and R2

•Isolated yields have varied between 10-3% to 10-8%•Anti-cancer properties: apoptosis induction, immune system booster, reverses multiple drug resistance, synergistic with other drugs•Currently in phase I and II clinical trials

Wender, P. A.; Hinkle, K. W.; Koehler, M. F. T.; Lippa, B. Med. Res. Rev. 1999, 19, 388.Suffness M, Newman DJ, Snader K. In: Scheuer PJ, editor. Bioorganic marine chemistry 3. New York: Springer- Verlag Publishers. pp. 131–168.Pettit, G.R.; Herald, C.L.; Doubek, D.L.; Herald, D.L.; Arnold, E.; Clardy, J. J Am Chem Soc 1982, 104, 6846.Pettit, G.R. J Nat Prod 1996, 59, 812.Pettit GR. Fortschritte 1991, 57, 153.

Bryostatin: Binding to PKC

Paul A. Wender, P. A.; De Brabander, J.; Harran, P. G.; Jimenez, J.-M.; Koehler, M. F. T.; Lippa, B.; Park, C.-M.; Shiozaki, M. J. Am. Chem. Soc. 1998, 120, 4534.Wender, P. A.; Cribbs, C. M.; Koehler, K. F.; Sharkey, N. A.; Herald, C. L.; Kamano, Y.; Pettit, G. R.; Blumberg, P. M. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7197.http://www.stanford.edu/group/pawender/html/synth.html

•Protein Kinase C (PKC) family of serine/threonine kinases is involved in signal transduction, and is important in the biochemistry of cancer•Bryostatin binds to PKC w/ high affinity

Bryostatin: Previous Total Synthesis

•Bryostatin 7 (R1=R2 = OAc) : Masamune, 1990•Bryostatin 2 (R1= OH, R2 = O2CC7H11) : Evans, 1998•Both total synthesis require >60 steps, making them untenable in process

Kageyama, M.; Tamura, T.; Nantz, M. H.; Roberts, J. C.; Somfai, P.; Whritenour, D. C.; Masamune, S. J. Am. Chem. Soc.1990, 112, 7407.Evans, D. A.; Carter, P. H.; Carreira, E. M.; Prunet, J. A.; Charette, A. B.; Lautens, M. Angew Chem Int.Ed. 1998, 37, 2354.

Wender’s Bryolog Targets

Wender, P. A.; Hinkle, K. W.; Koehler, M. F. T.; Lippa, B. Med. Res. Rev. 1999, 19, 388.Paul A. Wender, P. A.; De Brabander, J.; Harran, P. G.; Jimenez, J.-M.; Koehler, M. F. T.; Lippa, B.; Park, C.-M.; Shiozaki, M. J. Am. Chem. Soc. 1998, 120, 4534. http://www.stanford.edu/group/pawender/html/synth.html

•Hypothesis by Wender et al. (1988): pharmacophore region of byrostatin include C1, C19, and C26 oxygen atoms (bryostatin 1 Ki= 1.35 nM)

O O O

HH

HH

O O

O

O H

O R3

R1

C7H

1 5O CO

2Me

A) R1 = OH, R

2 = H, R

3 = OH

B) R1 = OH, R2 = H, R3 = OA c

C) R1 = H, R2 =OH, R3 = O H

D) R1 = H, R2 = H, R3 = OH

R2

Sp ecific Analog Targets

B A

C

O O O

R4

HH

H

O O

O

OH

O OH

HO

C7H1 5 O CO2 Me

B

C

E) R4 = H

F) R4 = t-B u

First Generation Sythesis of C Ring

O TBS

O O

O

OP MB

OB n

+4 steps

29%

from R-m ethy l lactatefrom methyl i -propy l ketone

O

OBn

OTB S

O H

HO

OM eOPM B

1) PhCOCl, DMA P; DMP

90%

2) Sm I2 90%

O

OBn

OTB S

O

OM eOPM B

1) LDA , CHOCO2 M e

2) M sCl, TEA3) DBU

70%

O

OB n

OTBS

O

OMeOP MB

CO2 M e

1) NaB H4 , CeCl

3 , -20 deg. C

2) C7 H1 5 CO 2H, Yam aguchi cond' ns

93%

O

O Bn

OTB S

O

OM eO PM B

CO2M eC7 H15 O

1) HF/pyr.2) DM P

86%

O

OB n

O

O

OMeOP MB

CO2M eC

7H

1 5O

1) a llyl -BE t2, E t2 O, -10 deg. C

2) A c2 O, DM AP

3) Os O4 , NM O4) P b( OAc )

4 , TE A; then DB U

76%

O

OB nO

O MeOP MB

CO2 M eC7H1 5 O

CHO

1) DDQ

2) HF, CH3 CN, H2 O

75%

O

OBnO

OHOH

CO2MeC

7H

1 5O

CHO

Paul A. Wender, P. A.; De Brabander, J.; Harran, P. G.; Jimenez, J.-M.; Koehler, M. F. T.; Lippa, B.; Park, C.-M.; Shiozaki, M. J. Am. Chem. Soc. 1998, 120, 4534.

First Generation Sythesis of “Spacer”Region

Wender, P. A.; Hinkle, K. W.; Koehler, M. F. T.; Lippa, B. Med. Res. Rev. 1999, 19, 388.Wender, P. A.; Baryza, J. L.; Bennett, C. E.; Bi, F. C.;. Brenner, S. E.; Clarke, M. O.; Horan, J. C.; Kan, C.; Lacôte, E.;Lippa, B.; Nell, P. G.; Turner, T. M. J. Am. Chem. Soc. 2002, 124, 13648.

O OHO

1) S wern2) t-B uLi3) DM P4) Luche reduction

dr = 6:1, 46%

O OHO

t-B u1) t-BuOK , a llylBr

2) 9- BBN; H2 O2 , NaOH3)DMP

72%

O OO

t-Bu

O

1) (- )-Ipc2B-CH

2CH=CH

2

2) TB SCl, imid.

3) cat. KM nO 4, NaIO4

42%

1) NaH, a llylBr 76%

2) 2) 9-BB N; H2 O2 , NaOH3)DM P

72%

1) (-)- Ipc2 B -CH2CH=CH2

2) TBS Cl , im id.3) cat. K MnO

4, NaIO

4

42%

O OO

O

O OO

R

O

OH

TB SO

R = H, t-B u

60% from pentanetrio l

1) Swern2) Danis hefsk y's d iene

O

ON

Cr

Cl

O OO

O

then TFA

1) Luche reduction

2) i-B uO CH=CH2 , Hg(OA c)2

3) Decane, 150 deg. C

76%

O OO

1) H2, Pd(OH)

2

2) (-)- Ipc2 B -CH2 CH=CH2

3) TBS Cl , im id.

4) KM nO4 , NaIO 4

49%

O OO

CHO

O

OH

TBS O

Completion of Analogs

O OO

O

OH

TB SO

O

OBnO

OHOH

CO2MeC

7H

1 5O

CHO

1) Yamaguc hi 81%

2) HF -py r. 81%

O

OO

HOO

O

O

OB nO

OH

CO2M eC7 H1 5 O

CHO1) Am berl ist- 15, rt, d i lu te

2) Pd(OH)2 , H2

88%

O OO

HOO

O

O

ORO

OH

CO2MeC

7H

1 5 O

A c2O, DM AP

85%

Bry olog A

R = H

Ki = 3 .4 nM

Bry olog BR = A c

Ki = 297 nM

O OO

R

O

OH

TBS O

1) Y am aguchi2) HF-pyr .

3) A mberlist-15, r t, d ilute

4) P d( OH)2, H

2

R = H, t-Bu

O OO

HOO

O

O

OHO

O H

CO2MeC

7H

1 5O

t-Bu

O OO

HOO

O

O

O HO

OH

CO 2M eC7 H1 5 O

Bry olog FK

i = 8 .3 nM

B ryolog E

K i = 47 nM

Wender, P. A.; Hinkle, K. W.; Koehler, M. F. T.; Lippa, B. Med. Res. Rev. 1999, 19, 388.

Role of C3 Hydroxyl

OO

HOO

O

O

OHO

OH

CO2MeO

MeO2C

HOOAc

Hydrogen bondingstabilizing a conformation?

O O

O

O

O

ORO

OH

CO 2M eC7 H1 5 O

O OO

HOO

O

O

ORO

O H

CO2M eC

7H

15O

O OO

O

O

O

ORO

O H

CO2 M eC7 H15 O

O OO

HOO

O

O

OHO

OH

CO2 MeC7H1 5 O

Br yolog A

Ki = 3.4 nM

Br yolog CK

i = 285 nM

B ryolog D

K i = 297 nMK

i > 10,000 nM

Wender, P. A.; Hinkle, K. W.; Koehler, M. F. T.; Lippa, B. Med. Res. Rev. 1999, 19, 388.

Fine-Tuning the Structure: SecondGeneration Sythesis of C Ring

OO

HOO

O

O

OHO

OH

CO2MeO

MeO2C

HOOAc

Are the methyl groupand the C26 stereocenter needed for activity?

Fine-Tuning the Structure: SecondGeneration Sythesis of C Ring

HO OH

1) NaH, TBS Cl

2) SO 3- py r., T EA, DM SO

3) M gClCH2 CH2 CH2 OMgCl

4) Swern

54%

3 k g = $34.80

TB SO

O O

1) R-BINOL, 4 A . M S, a llylS nBu3

T i(OiPr )4 , B (OM e) 3 77%

2) cat pTS A, 4 A . MS , P hMe 85%

3) MM PP , NaHCO3

M eOH/CH2 Cl2 78%, dr =4:1

O

HO

OM e

T BSO

H

CO3-

CO2H

2

M g2 +

M MP P

1) TP AP, NMO 78%

2) K2CO

3, CHOCO

2M e

MeOH 72% O

O

OMe

TB SO

H

CO2M e

O

O

OM e

TBSO

H

CO2Me

1) Luche r eduction2) C7 H1 5CO2 H, DIC, DMA P

93%

OC7H

1 5

1) 3HF-TE A

2) DM P, NaHCO3

87%

O

O

OM e

O

H

CO2M eOC

7H

1 5

t- BuLi, Me2Zn;

then 1M HCl

90%

O

O

OMe H

CO2M eOC

7H

1 5

1) (DHQD)2PYR, K

2Os O

2(OH)

4,

K3 Fe( CN) 6, K2 CO3 dr=2.5:1

2) pTSA

3) TBS Cl, im id.

46%

Br OE t

O

O

O

OH H

CO2 MeOC7 H1 5

O

OTBS

OH

Wender, P. A.; Baryza, J. L.; Bennett, C. E.; Bi, F. C.;. Brenner, S. E.; Clarke, M. O.; Horan, J. C.; Kan, C.; Lacôte, E.;Lippa, B.; Nell, P. G.; Turner, T. M. J. Am. Chem. Soc. 2002, 124, 13648.

Completion of Bryolog G

O OO

O H

O

TBS O

O

OTB SO

O HOH

CO2M eC

7H

15O

CHO

Y amaguc hi 87%

O

OO

TB SOO

O

O

OTBSO

OH

CO2 MeC7H

1 5O

CHO

O OO

HOO

O

O

OHO

OH

CO2 MeC7H

15O

HF-pyr

82%

Bry olog G

Ki = 0.25 nM

Wender, P. A.; Baryza, J. L.; Bennett, C. E.; Bi, F. C.;. Brenner, S. E.; Clarke, M. O.; Horan, J. C.; Kan, C.; Lacôte, E.;Lippa, B.; Nell, P. G.; Turner, T. M. J. Am. Chem. Soc. 2002, 124, 13648.

Comparison of Bryolog G toBryostatin 1

O OO

HOO

O

O

OHO

OH

CO2MeO

Bryolog GKi = 0.25 nM

OO

HOO

O

O

OHO

OH

CO2MeO

MeO2C

HOOAc

Bryostatin 1Ki = 1.35 nM

•Over 60 steps in previous syntheses of bryostatins•In phase I and II clinical trials•Cost (per previous synthesis): $2.3 million / g

•32 steps (longest linear = 20)•As effective or more effective than byrostatin 1 as an anti-cancer agent in most cases•Cost: $1400 / g

Migrastatin and Cell Migration•Anti-cancer agents mode of action is typically cell death•An alternative cancer therapy could rely on inhibition of cell migration•Cell migration is observed in a number of normal physiological processes (ovulation, wound healing, inflammation, embryonic development)•Cell migration also observed in tumor angiogenesis, cancer cell invasion, and metastasis

•Migrastatin was isolated by Imoto and Kosan bioscience researchers in 2000 from Streptomyces bacteria•Migrastatin has an IC50 of 29 µM in wound healing assays

Gaul, C.; Njardarson, J. T.; Shan, D.; Dorn, D. C.; Wu, K.-D.; Tong, W. P.; Huang, X.-Y.; Moore, M. A. S.; Danishefsky, S. J. J. Am. Chem. Soc. 2004, 126, 11326.

Retrosynthetic Analysis ofMigrastatin


M eO

M eO

O

O

O

O1) DIBAL-H, then ZnCl2, H2 CCHM gB r 75%, dr >9:12) M eI, NaH; then 2M HCl , MeOH 80%

OMe

OMe

OH

OHPb(OA c)4 Na2 CO3

OMe

O

1) T iCl4, -78 deg. C;

then T FA, rt 87% (3 steps )

2) L iBH4

3) CS A, H2O 4) L iBH

4 53% (3 steps)

MeO

OTM S

HO

OMe

OH

TB SOTf, 2 ,6-lu t.;

then HOAc , H2O, THF

80%

HO

OM e

OTBS

Synthesis of C7 to C13 Fragment

Gaul, C.; Njardarson, J. T.; Shan, D.; Dorn, D. C.; Wu, K.-D.; Tong, W. P.; Huang, X.-Y.; Moore, M. A. S.; Danishefsky, S. J. J. Am. Chem. Soc. 2004, 126, 11326.Jorgensen, M.; Iversen, E. H.; Paulsen, A. L.; Madsen, R. J. Org. Chem. 2001, 66, 4630.

Serendipitous Biproduct

•15% yield of this dimer biproduct obtained during Ferrier rearrangement when run at 0.3 M (scale-up conditions), though not significantly observed at 0.1 M (small scale conditions)•On the bright side, biproduct is crystalline


Attaching the Glutarimide Group

HO

OM e

O TBS

1) DM P

2) M gCl2 TE A, TMS Cl;

then TFA , M eOH

67%

N O

O

Bn

O

HO

OM e

O TBS

X c

O

1) T ESCl , imid.2) L iBH4

83%OM e

OTB S

OH

TE SO

OM e

O TBS

TES O

1) DMP ; then LiCH2 P (O)(O Me)2 ; then DM P2) L iCl, DBU, MeCN

57% NHO

O

O

O NH

O

O

Stry ker Rgt; then

HO Ac, H2O, THF

82%

HO

OM e

O TBS

O NH

O

O


Completion of Migrastatin


HO

OM e

OTBS

O NH

O

OYam aguchi (using pyr.instead of DM AP )

67%

OH

OO

O

NH

O

O

O

OTB S

OMe

G2 (20%), 0 .5 m MPhMe, re flux

69%

O

O

NH

O

O

O

OT BS

OM e

HF-py r.

85%

O

O

NH

O

O

O

OH

OM e

migrastatin

Derivitization of Migrastatin throughDiverted Total Synthesis


Synthesis/Evaluation (Cell MigrationAssay) of Migralogs A and B


O

O

NH

O

O

O

OTB S

O Me

HF-pyr.

81%

M eI, Cs2CO

3

acetone

85%O

O

NH

O

O

O

OH

O Me

O

O

NMe

O

O

O

O H

OM e

O

O

NH

O

O

O

OH

O Me

migr as tatin

IC5 0 = 29 µMStable in m ous e

b lood plas ma

X

S tr yker Rgt

M igra log A

IC5 0 = 10 µM

Stable in mouse

b lood p lasm a

M igra log B

IC5 0

= 7 µM

S table in m ouse

b lood p las ma

Simplified Migralogs C and DHave Improved Activity…


HO

Me

OTBS

Cl

O

1) DMAP

82%

2) G2 (20%), 0.5 mM PhMe, reflux 76%3) HF-pyr. 94%

1) Yamaguchi (using pyr. instead of DMAP)

48%2) G2 (20%), 0.5 mM PhMe, reflux 55%3) HF-pyr. 66%

OH

O

O

O

OH

OMe

Migralog CIC50 = 0.022 µM

Migralog DIC50 = 0.024 µM

O

O

OH

OMe

…But Are Quickly Hydrolyzed In Vivo

HO

Me

OTBS

Cl

O

1) DMA P

82%

2) G2 (20%), 0 .5 m M PhMe, re flux 76%3) HF-pyr. 94%

1) Yam aguchi (using pyr. instead of DM AP)

48%2) G2 (20%), 0 .5 m M PhMe, re flux 55%3) HF-pyr. 66%

OH

O

O

O

OH

O Me

Migr alog CIC

5 0 = 0.022 µM

Migr alog D

IC5 0 = 0.024 µM

O

O

OH

OM e

20 min. inc ubationin mouse b lood plas ma

5 m in. incubationin mouse b lood plas ma

O H

O

O H

OMe

M igra log E

IC50 not repor ted

M igra log F

IC50

= 0.378 µM

O H

O

OH

OM e

OH

OH


Stabilizing the Cyclic Core

HO

Me

O TBS

O

1) CBr 4 , P h3 P ( so lid supp.)2) DBU

then Na/Hg,

Na2 HPO 4, M eO H 61%

N

O

OTBS

OM e

Migra log G

IC50 = 0.255 µM

Stable in mouse

blood p lasm a

O

OT BS

OMe

1) (PhO)2P (O)N

3

DB U, P hM e 87%2) Ph

3P, H

2O ; then E DC,

DIE A, 6-heptenoic ac id 92%

1) G2 (20%), 0.5 mM PhM e, re flux 81%2) HF-pyr . 90%

SO2 P h

1) G2 (20%) , 0 .5 mM PhM e, re flux 60%2) HF-pyr . 81%

N

O

OH

OMe

O

OH

OMe

M igra log HIC

5 0 = 0.100 µM

S table in m ouse

b lood p las ma


Additional Reading:Halichondrin B and E7389

Aicher, T. D.; Buszek, K. R.; Fang, F. G.; Forsyth, C. J.; Jung, S. H.; Kishi, Y.; Matelich, M. C.; Scola, P. M.; Spero, D. M.; Yoon, S. K. J. Am. Chem. Soc. 1992, 114, 3163.Zheng, W. J.; Seletsky, B. M.; Palme, M. H.; Lydon, P .J.; Singer, L .A.; Chase, C. E.; Lemelin, C. A.; Shen, Y. C.; Davis, H.; Tremblay, L.; Towle, M. J.; Salvato, K. A.; Wels, B. F.; Aalfs, K. K.; Kishi ,Y.; Littlefield, B. A.; Yu, M. J. Bioorg. Med. Chem. Lett. 2004, 14, 5551.Paterson, I.; Anderson, E. Science 2005, 310, 451.

•Halichondrin B is a highly cytotoxic (antimitotic) marine natural product. Total synthesis: Kishi, 1992• Recent diverted total synthesis has led to simplified analog E7389 with similar antimitotic activity. Also, replacement of lactone with ketone has made E7389 more robust in vivo•E7389 currently in phase I clinical trials

diverted total synthesis in medicinal chemistry … total synthesis in medicinal chemistry research...

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