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A Career in Pharmaceuticals:
Drug Hunting in The Lipitor Era
Gregg M Kamilar
14C Radiosynthesis
Custom Synthesis of Radiolabeled Compounds
ViTrax – Placentia, CA
2011-2012
Labeled ROMP Monomer
High SA Polymer Substrate
High % Isotopic Incorporation via “Click Labeling”
Addressing Unexpected Isomeric Effects
Tetrahedron. 2004, 60, 11415-11420
Boranophosphate Nucleotide
Monomers
Building Blocks for RNAi Oligomer Synthesis
Pfizer, Inc – Cambridge, MA
2008-2009
Boranophosphates Delivered
Adenosine (N-BZ) 3.15 g
Cytidine (N-BZ) 3.56 g
Thymidine (N-BZ) 3.32 g
Guanosine (N-PAC)(O-DPC) 3.21 g
Optimizing Boranophosphorylation
Efficient
purification at this
step allows for use
of less pure
substrate
increasing
throughput
Working in 1 gram batches improves
reproducibility and yield
Short reaction times reduces side-
products
Partial purification preserves
overall yield
Protected Thymidine
Nucleosides, Nucleotides and Nucleic Acids, 20:12, 1927 - 1939
Protected Guanosine
J. Org. Chem. 2004, 69, 5261-5268
Boranophosphorylating Reagent – Literature Method
•3 steps/3 purifications
•Isolation of phosphite
triester was problematic
J. Am. Chem. Soc., 98, 7327 (1976)
Boranophosphorylating Reagent – Modified method
•2 steps/2 purifications
•No isolation of phosphite triester
•Scaled successfully to >25 g
•Final salt is highly stable oil @ RT
J. Am. Chem. Soc., 98, 7327 (1976)
Literature Synthesis of MNTP Condensing Reagent
Key
Intermediate
Tetrahedron 62 (2006) 3667–3673
Alternate Synthesis of The Key Intermediate
J. Am. Chem. Soc. 1967, 89, 6276–6282
Aldrich
D15,780-5
$4.48 - 7.89 / gram
Completed Synthesis of MNTP
J. Am. Chem. Soc. 1967, 89, 6276–6282
Tetrahedron 2006, 62, 3667-3673
Aldrich
D15,780-5
$4.48 - 7.89 / gram
2’-Cyclopropyl Nucleotide
A Building Block for RNAi Oligomer Synthesis
Pfizer, Inc – Cambridge, MA
2009
Route to 2’-Cyclopropyl U and C
J. Org. Chem., Vol. 62, No. 5, 1997
CAN. J. CHEM. VOL. 71, 1993, p 413
Scaled Synthesis of Starting Ketone
Can. J. Chem. Vol 44 , 1966, p. 836
Mitsunobu Protection of Uridine O4
J. Org. Chem., Vol. 62, No. 5, 1997
Scaled Cycloaddition
Modified from
Org. Syn. 1935, 16, 3
Can. J. Chem. Vol 44 , 1966, p. 836
H3C
NH
N
N
O
HN N+
O-
O
Conversion to Cyclopropane
Can. J. Chem. Vol 44 , 1966, p. 836
Undesired Glycosidic Cleavage
Can. J. Chem., 1993, 71, 413
Heterocycles, 2003, 59, 207
Substrate Effects in Deprotection
N
OEt
O N
O
TBDMSO
TBDMSO
HN
O
O N
O
OH
HO
N
OEt
ON
O
O
OSi
Si
O
N
OEt
ONH90 ºC
O
OH
HO
+
OMe
RT
OBz
OBz
OMe
OBz
OBz
83%
10 : 1
MeOH : 1 M HCl
10 : 1
MeOH : 1 M HCl
N
OEt
ON
O
OH
HO
RT
Heterocycles, 2003, 59, 207
New Protection Strategy for Uridine
J. Am. Chem. Soc. 1992, 114, 4008-4010
J. Med. Chem., 1991, 34, 999-1002
1) Benzoyl group can be left on until final oligo deprotection
2) Can be removed under mild conditions prior to phosphitylation
3) Installation is a high yielding reaction
Synthesis and SAR of A Bacterial
Translation Inhibitor
Pharmacia, Inc – Kalamazoo, MI
1999-2003
C
B
A
OH
NH
O
Br
O
N ClO
OS
Ring substitution
Meta is better
Heterocycles
Ring substitution
Isosteric carboxylic
acid replacements
Linkers
Ring substitution
Other Sulfonamides
Linkers
A Three Ring Pharmacophore
R6
R2
R5
R4
N ClO
OS
R6 R5
R4
R2
N ClO
OS
NH (COCl)2
N 2H
Cl
Py
CH2Cl2
CH2Cl2Py
CH2Cl2
Br
O
O
LiOH
Dioxane
40 oC
BrBr
R6
R5
R4 R2
R6
R5
R4
R6
R5
R2R4
R2
OH
NH
O
O
O
NH
O
O
CO2Cl
Cl
OO
N
S
COOH
SO2Cl
S
N
O O
Cl
COOH
Synthetic Route
GG
GG
65o-120 oCSO2Cl
CO2H(Me)CO2H(Me)
HSO3Cl
65o-120 oCSO2Cl
CO2H(Me)CO2H(Me)
HSO3Cl
Direct o/p Chlorosulfonation
G G G
GGG
CO2Me
N 2H
CuCl . 2H2OCO2Me
Cl-
CO2MeHClAcOH
NaNO2
5 oC
AcOH
SO2(g)
-10 oC
H2OSO2Cl
NN
+
+
CO2Me
N 2H
CuCl . 2H2OCO2Me
Cl-
CO2MeHClAcOH
NaNO2
5 oC
AcOH
SO2(g)
-10 oC
H2OSO2Cl
NN
+
+
Organic Syntheses, Vol 60, p.121, (1981)
m/o Chlorosulfonation via Diazotization
N
Cl
HN
Cl
HNaCNBH3
AcOH
1) (COCl)2 / DMF
CH2Cl2
2) LiOHDioxane
N 2H
COOMeBr N
N 2H
COOMeC
COOH
SO
N
O
Cl
SO2Cl
COOH
Reflux
NMPCuCN+
MeOH
Et3N
PHA-xxx523
SAUR MIC 0.125 g/mL
2 g/mL in 5% serum
Ratio = 16
Cl
N C
OH
H
O
O
N
ON
OS
Convergent Synthesis of Cyanoanthranilic Acids
N 2H
~ 15 gram scale
1) HNR'R", base
2) Deprotect acid
2R
PO
O
CH2Cl2
Py
ClSO3H
80 °C CH2Cl2
DMF
(COCl)2
Cl
ClS
O
O
ON
O
OH
ClS
O
O
ON
O
ClS
O
O
OEt
ON
O
OEt
ON
O
OH
O
O
ON
SOO
N
N
H
2R
R'R"
PHA-xxx228
External CRO
2R
H
N
PG
Cl
OO S
N O
O
O
further heating
Synthesis of a Versatile Intermediate
R"R'
N
OO S
N O
O
CN
O
OH
NH
Cl
OO S
N O
O
CN
O
BnO
NH
Cl
OO S
N O
O
CN
O
t-BuO
NH
N
OBnO
N 2H
C
Ot-BuO
N 2H
CN
X
ClS
O
O
ON
O
1. HNR'R"2. TFA
1. HNR'R"
2. H2, Pd/C(COCl)2
DMF
CH2Cl2
CH2Cl2, reflux
X = OH
X = Cl
METHOD B
METHOD A
Parallel Routes Afford Diversity
Synthesis of A Novel
Bacterial Gyrase Inhibitor
Pharmacia, Inc – Kalamazoo, MI
2004-2005
Verboom, W.; Reinhoudt, D. N.;
Visser, R.; Harkema, S. J. Org.
Chem. 1984, 49, 269-276.
[1,5] Hydride Shift
H
H
H
N+
O-
O
O
NHNH
O
O2N
NH
NH
O
O
O
H
O
N
O2N
O
O-O
NHNH
O
N+
O2N
O
OO
NHNH
O
N
O2N
Mechanism of Alkylidene Cyclization
2,6-Dimethylmorpholine is the only commercial 2,6-disubstituted morpholine.
Beilstein search reveals only 2 other 2,6-disubstituted morpholines.
Symmetrical cis morpholines are meso.
Non-symmetrical morpholines have regioselectivity problems in final step.
Cis and trans isomers difficult to separate.
Asymmetric synthesis is highly unlikely.
Morpholines are volatile.
Intermediates Made by Classical Morpholine Synthesis-
J. Het.Chem. 1977, 14, 899-904
NH
O
RNH
R
OHOH H2SO
4
N
O
Bn150 ºC
Classical Morpholine Synthesis
NH
NH
N
O
O
O
O
H
O2N
NH
NH
N
O
O
O
O
H
O2N NH
NH
N
O
O
O
O
H
O2N
NH
NH
N
O
O
O
O
H
O2NNH
NH
N
O
O
O
O
H
CF3
O2N
NH
NH
N
O
O
O
O
CF3
H
O2N
Racemic Non-Symmetrical Analogs
N
O
O
Cl
Cl
O
N
O
ClH
F
H
O
NO2
N
O
H
O
NO2
1) CH2Cl2, RT
2) MeOH, reflux
(2S,6S)-(-) (2S,6S)-(-)
Hunig'sK2CO3
CH3CN
reflux
Unpublished
NH NH
O
O ONH
NH
N
O
O
O
O
H
O2N
(2S,4S,4aS)-(-)-
CH3OH
reflux
Finishing the Asymmetric Synthesis
[1,5] hydrideshiftH
Me
Me
CF3
Me
CF3
CF3
H
O-
O
O
NHNH
O
HO2N
N+
H
O-
O
O
NHNH
O
HO2N
N+
CF3
CF3O
-
O
O
NHNH
O
O2N
N+
H
O2N
H
O
O
OMe
O
N
NH
N
H
O2N
H
O
O
O
Me
O
N
NH
N
Favored?
Regioselectivity via Non-Symmetrical Morpholines
RacemicCommercial
CH3CN
RT
TEA
CH2Cl2
0o C
F3C
F3CF3C
BrO
OH
N
ClBr
OOH
HN
N 2H
O
++
Cl
K2CO3
CH3CN
reflux
NO2
H
OF
60o
0o - RT
ClHNH
F3C O
O
ClO
F3C
N
OF3C
N O
O
LAH/THFNaH/THF
MeOHreflux
O2N
H
O
O
OCF3
O
N
NH
NH
O2N
H
O
O
O
CF3
O
N
NH
NHF3C
O
OO
NHNH
H
O
O
NO2
N
88 : 12
A Regioselective Synthesis
ON
O
Me
Me
HN NH
O O
O
[1-5] shift
N
HNH
NH
O
O
OCH3
CH3
Ha
Hb
O
N
Ha HN
NH
O
O
OCH3
CH3
Hb
O
H
HN
OCH3
CH3
NHHN
O
O
O
Hb
Ha H
bond rotation
N O
Hb
H Ha
CH3
CH3
NH
HN
O
O
irreversible
N
OCH3
CH3
NHHN
O
O
O
Hb
Ha H
O2NO2N O2N
O2N
O2N
O2N
N
O
Me
Me
O
O2N
1
9
10a 11
10b 12
PNU-286607
[1,5] Hydride Shift Mechanism
