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IV. Combinatorial Chemistry
1. Library synthesis
a) in solution, parallel synthesisb) on solid supportc) split and combine, one bead one compound
2. Deconvolution and Tagging
3. Dynamic Combinatoric Chemistry
diversification reaction
diversification reaction
divide
Parallel Library Synthesis
• 12 reactions provide 9 compounds
• The library members are spatially separated, so this technique can be used for solution as well as solid phase synthesis
split pool and splitdiversification reaction
diversification reaction
Split-pool Synthesis
• 6 reactions lead to 9 compounds
• Each library member must be compartmentalized (each compound on its own bead) to allow pooling of the library
O
NHBoc
SnMe39X
O
NHBoc
SnMe3
O
NHBoc
SnMe3
O
NHBoc
SnMe3
3X
3X
3X
1) Pd2dba3,
2) TFA
1) Pd2dba3,
2) TFA
1) Pd2dba3,
2) TFA
Cl Me
O
Cl
O
Cl
O Cl
O
NH2
3XO
Me
O
NH2
O
3X
O
NH2
O
3XCl
O
NH2
O
Me3X
O
NH2
O
3X
O
NH2
O
Cl3X
split pooldiversification reaction
Ellman, J. et al. J. Am. Chem. Soc., 1995, 117, 3306.
An Example of Split-Pool Synthesis
O
NH2
O
Me
O
NH2
O
O
NH2
O
Cl
O
NH2
O
Me
O
NH2
O
O
NH2
O
Cl
O
NH2
O
Me
O
NH2
O
O
NH2
O
Cl
F
O
NHFmoc
F
O
NHFmoc
F
O
NHFmoc
CO2H
S
1)
1)
1)
2) piperidine
2) piperidine
2) piperidine
O
NH
O
MeO
NH
O
O
NH
O
Cl
ONH2
ONH2O
NH2
O
NH
O
Me
O
NH
OO
NH
O
Cl
ONH2
ONH2
ONH2
HO2C
HO2CHO2C
O
NH
O
Me
ONH2
O
NH
O
ONH2
O
NH
O
Cl
ONH2
S
SS
split diversification reaction
Ellman, J. et al. J. Am. Chem. Soc., 1995, 117, 3306.
Overview of the Entire Split-Pool Library
O
NH2
O
R1O
NHBoc
SnMe3
Cl R1
O
Pd2dba3,TFA
F
O
NHFmoc
2) AcOH
R2
O
NH
O
R1
ONHFmoc
R2
O N
HN
O
R2
R1
1) piperidine Base, R3X TFA
O N
NO
R2
R1
R3
20 Acid Chlorides
35 Amino Acids
16 Alkylating Agents
20 cpds 20 x 35 = 700 cpds
700 cpds 20 x 35 x 16 = 11,200 cpds
Split-Pool step:
Schreiber SL et al. JACS, 1998, 120, 8565.
O O
N
H
HO
O
HN
O
I
R2 NH2
62 amines
O
N
O
HN
O
R1
O
O
NHR2
O
R3
62 acids
R3
O
OH
30 + 62 + 62 = 154 reactions18 X 30 X 62 X62 = 2.1 million compounds
R1
30 alkynesO O
N
H
HO
O
HN
O
R1
O
N
O
HN
O
R1
HO
O
NHR2
18 iodides
Example of the Efficiency of the Split-pool Strategy
• Optimization of 154 reactions affords 105 amplification in the number of compounds
Structural Characterization: Direct Methods
Off-bead Analysis• Cleavage, then use of analytical techniques used in TOS (e.g. LC, MS,
NMR)• Requires high sensitivity and high throughput format
• Example: LC-UV/ MS
S
OH OH
N
O
HOPh
Ph
Structural Characterization: Direct Methods
On-bead Analysis I• Can be used to monitor the progress of a reaction • MAS-NMR ( Magic angle spinning NMR ) is necessary due to polymer
Magic angle rotor (left), rotor spinning at the magic angle (right)
MAS- NMR spectrum (600 MHz)
OO
Si
O
O
OMe
O
OOO
Structural Characterization: Direct Methods
On-bead Analysis II• Example: Single-bead FT-IR microspectrometry• Can be used to monitor the progress of a reaction
O
O
DIC, DMAP, DMFO
O
O OH
HO
O O
Beads in IR cell
Wavelength(cm-1)
Structural Characterization: Indirect Methods
Deconvolution• Screen as a mixture of
compounds then re-synthesize and re-assaypossible candidatesin active pools
Drawbacks:• Interference by
unwanted propertiesof other compounds(e.g. cytotoxicity)
• Possible synergisticinteraction of multiplecompounds
• Sub-library synthesisis cumbersome
Encoding
• Encoding should provide a fast and simple way to identify the structure of all library members
• Classification– Spatial encoding: position of the compound provides the information about
its structure (possible only in parallel synthesis)– Graphical encoding: bar codes or other graphical tags are displayed on the
solid support used in the library synthesis– Chemical encoding: every reaction used in the library synthesis is recorded
on the solid support by the chemical attachment of a tag • binary coding (presence or absence of a tag) or polymer based
(polypeptide, DNA)– Spectrometric encoding: using a spectrometric technique (NMR, MS,
Fluorescence microscopy, NMR etc.) to read tags directly from the solid support
– Electronic encoding: radio frequency memory chip attached to the solid support records and emits coded information
A. C. Czarnik Current. Opp. Chem. Biol. 1997, 1, 60
split pool and splitdiversification reaction
diversification reaction
Encoding in Split-pool Synthesis
• Optimization of 6 reactions leads to 9 compounds
• Each library member must be isolated on its own bead to allow pooling of the library
How do you know what compound is on a given bead after a pool step?
Chemical Encoding in Split-Pool Synthesis
• Every diversification reaction is followed by a tagging reaction in which a tag(s) that codes for a particular transformation is covalently attached to the solid support
Decoding
• Every bead has tags that provide information, once cleaved, about the chemical history of that bead
• Conditions for cleavage of compound and tags have to be orthogonal
small molecule
compound cleavage tag cleavage
Binary Chemical Coding
11 10
00 01
Buildingblocks
Tags
001 010 100
011 110101 111
0
1
11 110 1
Binary(base 2)codon
2 digit codon22 = 4 max
3 digit 1 digit
n binary tags code for 2n building blocks
Another Example
00 01 001 010 100 0
BuildingBlocks
Tags
11 10 011 110101 111 1
10 011 0
Halogenated Aromatics As Tags
• Small amount of tag can be reliable detected (0.5-1 pmol/bead) using easily automated electron capture GC in the mixture of tags based on different retention times
• Inert under most reaction conditions
O O
n
Cl
Cl
X
Cl
XX=Cl or H
N2HC
O
OMe
linker variableregion
variableelectrophore
W. C. Still et al. J. Org. Chem. 1994, 59, 4723
Attachment and Cleavage of Tags
• Tags are attached using rhodium carbene-insertion chemistry and can be cleaved using (NH4)Ce(NO3)6 (CAN)
Si O
MeMeMe
Me
MeMe
Me
Si O
Me
O(CH2)nOCl
X
ClX
ClOMeO* small molecule
HF cleavable
TAGCAN
cleavable
* small molecule
O(CH2)nOCl
X
ClX
ClOMeO
N2HC
Rh2(O2CC(Ph)3)4
CH2Cl2, 25 °CCycloheptatriene
X = H or Cl
n = 1-14
TAG
Binary Chemical Encoding of a Peptide Library
• A library of decapeptides was synthesized and screened for binding to 9E10 mAb.
• 7 Amino acids were used at each position (S, I, K, L, Q, E, D)
• Every amino acid was assigned a 3 digit binary codon (001=S, 010=I, 011=K, 100=L, 101=Q, 110=E, 111=D) where 1=presence of a tag and 0=absence
• For each step in the library synthesis there are 3 tags designated nX (total of 18 tags for a library of 117,649 members, maximum encodable is 218 = 262,144)
HO2C
NO2
O O OArx
O
linker electrophoric tag
n
nX general formula of tags used
H2N-X-X-X-X-X-X-E-E-D-L-G-G-G-G-EQKLISEEDL known to bind 9E10
110 101 011 100 010 001 identified as the best binder
W.C. Still et al. PNAS 1993, 90, 10923
Dynamic Combinatoric Chemistry
Virtual Dynamic Combinatoric Library
Virtual Dynamic Combinatoric Library - macrocycles
Virtual Dynamic Combinatoric Library – carboanhydraseinhibitors
Lehn et al. 2106
Virtual Dynamic Combinatoric Library
Lehn et al. 2106
Virtual Dynamic Combinatoric Library – metal grids
Lehn et al, PNAS, 2003, 100, 11970
Virtual Dynamic Combinatoric Library – metal grids
Lehn et al, PNAS, 2003, 100, 11970
Virtual Dynamic Combinatoric Library – neuraminidase inhibitors
Eliseev et al, PNAS, 2002, 99, 3382
Virtual Dynamic Combinatoric Library – neuraminidase inhibitors
Eliseev et al, PNAS, 2002, 99, 3382
Virtual Dynamic Combinatoric Library – acetylcholine esterase inhibitors
Sharpless et al, PNAS, 2004, 101, 1449
Bourne, Yves et al. (2004) Proc. Natl. Acad. Sci. USA 101, 1449-1454
Pseudodynamic Dipeptide Library
Angew. Chem. Int. Ed. 2004, 43, 2432.
Protease from Streptomycesgriseus
Pseudodynamic Dipeptide Library
Angew. Chem. Int. Ed. 2004, 43, 2432.
Pseudodynamic Dipeptide Library
Angew. Chem. Int. Ed. 2004, 43, 2432.
CA = carbonic anhydrase
V. Diversity Oriented Synthesis
Molecular Complexity
Divergent Synthesis – Diversity oriented synthesis (DOS)
• complexity-generating rxns.• multicomponent coupling• diversity-generating rxns.
Synthesis planning:forward synthetic
analysis
manydifferent
molecules
Convergent Synthesis – Target oriented synthesis (TOS)
• complexity-generating rxns.
• fragment coupling rxns.
Synthesis planning:retrosynthetic
analysisonemolecule
TOS: Retrosynthetic Analysis of Saframycin A
A. G. Myers and D. W. Kung J. Am. Chem. Soc. 1999, 121, 10828.
Me
N
N
H
O
OO
O
Me
MeO
CNNH
Me
OO
H
Me
OMe
H
saframycin A
Me
N
N
H
HO
OMeOMe
OH
Me
MeO
CNNHFmoc
H
Me
OMe
H
IntramolecularStrecker Reaction
Me
NH
N
H
HO
OMeOMe
OH
Me
MeO
H
Me
OMe
H
FmocHNNC N
O
2 pictet-spengler reactions
H2N
N
HO
OMeOMe
OH
Me
MeO
H
Me
OMe
NC N
O
H
CHO
FmocHN
NH2
OMe
OH
Me
MeO
HCHO
NH
OMe
OH
Me
OMe
HOHC
HCN HN
O
Imine formation andStrecker reaction
NHFmoc
OMe
OTBS
Me
MeO
HCHO
NNH2
OH
Me O
Me
1. LHMDS, LiCl, 0ÞCTHF
2. OMe
OTBS
Me
MeO
Br
0ÞC
NNH2
OH
Me O
Me
MeO
Me
OMe
OTBS
89% de
LiH2N-BH3
THF
NH2
MeO
Me
OMe
OTBS
HONHFmoc
MeO
Me
OMe
OTBS
HOFmoc-Suc
NaHCO3
NHFmoc
MeO
Me
OMe
OTBS
O
H
Dess-MartinPeriodinane
CH2Cl2
80% yieldpseudoephedrine
A. G. Myers, P. Schneider, S. Kwon, D. Kung J. Org. Chem. 1999, 64, 3322.
Pseudoephedrine as a Chiral Auxiliary for Enolate Alkylation
TOS: A Concise Synthesis of Saframycin A
Myers and Kung JACS, 1999, 122, 10828.
X = H
X = MeCH2O, NaBH(OAc)3
X
RHN
N
H
HO
OMeOMe
OTBS
Me
MeO
H
Me
OMe
H
NC N
O
H
94%
Me
H2N
N
H
HO
OMeOMe
OH
Me
MeO
H
Me
OMe
H
NC N
O
H
TBAF, HOActhen DBU, 23ÞC
92%
R = Fmoc =
O
O
Fragmentcoupling
LiBr
DME35ÞC65%
NHR
OMe
OH
Me
MeO
HCHO
NH2
OMe
OH
Me
OMe
HRHN
N
TBSO
OMeOMe
OTBS
Me
MeO
H
Me
OMe
NC N
O
HN
NC
O
H
protectedaldehyde
H
Na2SO4
CH2Cl223ÞC
92% ee
96% ee
90%
Myers and Kung JACS, 1999, 122, 10828.
TOS: A Concise Synthesis of Saframycin A
Me
NH
N
H
HO
OMeOMe
OH
Me
MeO
H
Me
OMe
H
NC N
OFmocHN
Me
H2N
N
H
HO
OMeOMe
OH
Me
MeO
H
Me
OMe
H
NC N
O
H
CHO
FmocHNNa2SO4
CH2Cl223ÞC66%
Me
N
N
H
HO
OMeOMe
OH
Me
MeO
CNNHFmoc
H
Me
OMe
H
TFA, THF, 23ÞC
ZnCl2, TMSCN
86%
Me
N
N
H
O
OO
O
Me
MeO
CNNH
Me
OO
H
Me
OMe
H
saframycin A
1. DBU2. ClCOCOCH3,PhNEt2
3. PhIO, MeCN-H20
52%
Why Perform Diversity-Oriented Synthesis?
• To systematize the discovery of molecules with properties that are difficult to design or predict.
• DOS is especially useful in cases where processes are complex and few of the “design”criteria are well understood. For example:
• Asymmetric catalysis.• Small molecules with specific biological functions (protein binding,
cellular effects).
• DOS approaches are useful when molecules that act through new mechanisms are desired. This is useful because it may illuminate aspects of chemistry or biology that have not yet been illuminated. It is possible because the screen may make no assumptions about mechanism. For example, a DOS approach could be used to discover Diels-Alder catalysts that work by an unexpected and completely novel mechanism and in the process illuminate new meansof promoting cycloaddition reactions.
Screen for molecule(s)with desired properties
N N
N
Me Me
MeO SH
CO2H
Discovery of molecule withdesired properties
StudyMechanism;understand
chemistry or biology
N
OH
O
NH2
O
CO2H
S
N N
N
HN
OEt
Me O
NH2
NH
CHO
Me O
O
NH2
O
HO
Me Me
MeO SH
CO2H
Synthesis of diverse molecules:Molecules may be biased towards properties that will
achieve the goal (e.g. protein-binding elements or metal binding elements
DOS: Synthesis, Screen, Discover, Study
M e
O H
R R
O A c O Hacylationcatalyst
A c 2 O
racemic
FeN
Me2N
Ph
PhPh
Ph
Ph
P
MeMe
H
H
Me Ar
9 steps;not easily modified;
limited scope of benzyl alcohols;S = 15-389!
7 steps; separation by chiral HPLC;not easily modified
S = 43-65 with benzyl alcohols;S = 14-22 with allylic alcohols
G. Fu Acc. Chem Res . 2000 , 33 , 412.J. Ruble, H. Latham, G. Fu J. Am. Chem. Soc. 1997 , 119 , 1492.
E. Vedejs, O. DaugulisJ. Am. Chem. Soc. 1999 , 121 , 5813.
Target-Oriented Synthesis Approach
DOS vs. TOS in Enantioselective Catalysis (Example 1)
BocHN
HN
NMeN
O
NH
HN
NH
HN
NH
O
O
O
O
OiPr
iPr
HN
iPr
MeO
OMe
O
CONHR
NR
16 steps-easily synthesized via amide coupling reactions on solid phase;structure easily modified;
Diversity-Oriented Synthesis Approach
G. Copeland and S. Miller J. Am. Chem. Soc . 2001 , 123 , 6496.
M e
O H
R R
O A c O Hacylationcatalyst
A c 2O
racemic
DOS vs. TOS in Enantioselective Catalysis (Example 1)
An Example of DOS: Discovery of New EnantioselectiveAcylation Catalysts for Kinetic Resolution
BocHN
HN
NMeN
O
NH
HN
NH
HN
NH
O
O
O
O
OiPr
iPr
HN
iPr
MeO
OMe
O
CONHRNR
Krel=KR/KS=20(95% ee at 48% conv)
Copeland and Miller J. Am. Chem. Soc. 2001, 123, 6496.
Fluorescent beads=active catalysts
selectbrightestbeads
Me
OHMe
Me
OAc
OH
catalyticlibrary
Ac2OPhCH325ÞC
100,000 of 146 (7.5 million)catalysts made
BocHN
HN
AA6
NMeN
O
AA5 AA4 AA3 AA2 AA1 NH
MeHN
ONH
O
N
D-Val, D-Phe, D-Pro, L-Ile, L-(OtBu)-Tyr, L-(trt)-GlnD-Ala, L-(trt)-Asn, Gly, Aib, L-(OtBu)-Asp, L-(Boc)-Trp
L-(trt)-His, D-(OtBu)-Glu
500μMbead
biasingelement
for acylation
fluorescencedetector of AcOH
otherfunctionality Gen. Base
H-Bond
R2
π-Stack
NH
NUC
R
O
O
R
R1
OH
O
Me O
otherfunctionality Gen. Base
H-Bond
R2
π-Stack
NH
NUC
R
O
O
R
R1
OH
O
Me O
versus
TS1 TS2
Plan for Discovery of Enantioselective Peptide-Based Acylation Catalysts
Include Amino Acids with Desireable Properties, but use Approach that is Modular and Variable
catalyst
HN
N
O
Non-Fluorescent
catalyst
HN
N
O
Fluorescent
H
R1 R2
OH
R1 R2
OAc
Ac2O
Brightest Beads Contain Most Active Catalysts
Split-Pool Diversity-Oriented Synthesis of Acylation-Biased Peptides
BocHN
HN
AA6
NMeN
O
AA5 AA4 AA3 AA2 AA1 NH
MeHN
ONH
O
N
D-Val, D-Phe, D-Pro, L-Ile, L-(OtBu)-Tyr, L-(trt)-GlnD-Ala, L-(trt)-Asn, Gly, Aib, L-(OtBu)-Asp, L-(Boc)-Trp
L-(trt)-His, D-(OtBu)-Glu
500μMbead
biasingelement
for acylation
fluorescencedetector of AcOH
H2N
MeHN
ONH
O
N
500μMbead
O
OHFmocHN
R
HBTU, iPr2NEtDMF, 25ÞC
1 AA in each of16 different flasks
NH
MeHN
ONH
O
N
500μMbead
FmocHN
O
R
pool into one flaskN
H
DMF
split into 16 flasksNH
MeHN
ONH
O
N
500μMbead
H2N
O
R
repeat 6 times
H2NAA6 AA5 AA4 AA3 AA2 AA1 N
H
MeHN
O
500μMbead
BocHN
HN
AA6
NMeN
O
AA5 AA4 AA3 AA2 AA1 NH
MeHN
O
500μMbead
HBTU, iPr2NEtDMF, 25ÞC
BocHN
NMeN
O
OH
Me
OHMe
OAc
Me
OHMe
OAc
Me
OH
Me
OAc
MeMe
OHMe
Me
OAc
Ac2O, PhMe, -65ÞC
krel = 20
Ac2O, PhMe, -65ÞC
krel = 50
Ac2O, PhMe, -65ÞC
krel = 9.0
Ac2O, PhMe, -65ÞC
krel = 4.0
cat.
cat.
cat.
cat.
BocHN
HN
NMeN
O
NH
HN
NH
HN
NH
O
O
O
O
OiPr
iPr
HN
iPr
MeO
OMe
O
CONHRNR
cat. =
Discovery of Powerful Enantioselective Acylation Catalysts
This peptide-based catalyst would have been impossible to design - DOS leads to a discovery.
Use of a DOS-Catalysis Approach in Complex Molecule Synthesis
N
O
O
Me
H2N OMe
O
NH2O
NH
mitomycin C
N
OO
O
N
OOO
OtBuO
OtBuO
N
OHOO
OtBuO
Cl2Ru
Cy3P Ph
NN IMesIMes
CH2Cl2, 55ÞC
LiAlH4
Et2O
NH
HN
BOC
N
N
Me
O
NH
R1O
HNO
R2R3
(Xaa)n
O OMe
NH
N
BOC
N
N
Me
O
NH
O
HNO
Ph
NH
PhO
CO2Me
Ph
DOS and Screenof 152 peptides
CAT
N
OHOO
OtBuO
N
OAcOO
OtBuO
N
OHOO
OtBuO
Ac2OPhCH3
2 mol% CAT
S = 9.8 =90% ee @ 53% conversion
+
BocHN
HN
NMeN
O
NH
HN
NH
HN
NH
O
O
O
O
OiPr
iPr
HN
iPr
MeO
OMe
O
CONHRNR
previously optimized catalyst only produces S = 5.0
S. J. Miller et al. Organic Letters; 2001; 3(18); 2879-2882
Enantiospecific Synthesis of a Mitomycin Core Structure
N
O
O
Me
H2N OMe
O
NH2O
NH
mitomycin C
N
OHOO
OtBuO
N
OO
OtBuO
O
ON
OMeO
O
N
OMeO
N3
OH
N
OMeO
N3
OMs
N
OMeO
NH
1. Oxone, NaHCO 3acetone-H 2O
2. (ClCO) 2, DMSOEt3N, CH2Cl2
HNO3, MeOH Sm(OiPr) 3, TMSN 3
MsCl, Et3N
CH2Cl2
CH2Cl2
resin bound PPh 3
iPr2NEt, THF-H 2O
S. J. Miller et al. Org. Lett. 2001
85%
81%
86%
42%, 2 steps
O
nn = 1-3
O
n R
cat. Cu Saltcat. ligand
R2Zn
DOS vs. TOS in Enantioselective Catalysis (Example 2)
Target-Oriented Synthesis Approach
O
OP N
Me
Me
B. Feringa et al. Angew. Chem. Int. Ed. Engl. 1997, 36, 2620.
98% ee with wide range of 6-membered ringshowever, low ee for 5 and 7-membered rings;
the structure is not easily modified
O
Me10% ee
O
Me
53% ee
Difficult Substrates
Ligand structure optimizationIs difficult and time consuming
3 steps-easily synthesized via amide coupling reactions;structure easily modified;
Diversity-Oriented Synthesis Approach
S. Degrado, H. Mizutani, and A. Hoveyda J. Am. Chem. Soc. 2001, 123, 755.
N
HN
NHBu
Me Me
PPh2O
Ph
O
72-98% ee with wide range of 5,6, and 7-membered rings
O
Me
Me
O
MeMe
O
Me
Me
79% ee
72% ee 62% ee
Difficult Substrates
biasing element for metals
Rapid ligand optimization using DOSapproach
O
nn = 1-3
O
n R
cat. Cu Saltcat. ligand
R2Zn
DOS vs. TOS in Enantioselective Catalysis (Example 2)
The DOS approach allows optimization
S. Degrado, H. Mizutani, and A. HoveydaJ. Am. Chem. Soc. 2001, 123, 755.
O
nn = 1-3
O
n R
cat. Cu Saltcat. ligand
R2Zn
N
HN
NHBu
Me Me
PPh2O
Ph
O
O
Me
Me
O
MeMe
O
Me
Me
79% ee
72% ee 62% ee
Difficult Substrates
rapid ligand structure optimizationbecause it was discovered using DOS approach
positional optimization strategy
N
HN
NH
Me Me
PPh2O
OMe
OtBu
O
OMeN
HN
NHBu
Me Me
PPh2O
OMe
OtBu
O
Me
Me
81% ee
O
Me
Me
91% ee
AA1AA2
AA3
O
MeMe
85% ee
The positional optimization strategy involves optimizing each AA individually while holding the others constant
Use of DOS to Discover Enantioselective Catalysts of the Strecker Reaction (Example 3)
H
N
CN
NF3C
O
HCN
1. catalyst2. TFAA
+ *
P
P N
O
N
O
R R
NN
R R'
OM
O
binap bisoxazoline salen
These ligands that are common in asymmetric catalysis are not well suited for a DOS approach since:1. They do not provide a nonobtrusive site for attachment to the solid-phase2. They are not condusive to wide structural variations (diversity)
M
M
PhPh
PhPh
Use of DOS to Discover Enantioselective Catalysts of the Strecker Reaction (Example 3)
Sigman and Jacobsen JACS, 1998, 120, 4901.
P
P N
O
N
O
R R
NN
R R'
OM
O
binap bisoxazoline salen
These ligands that are common in asymmetric catalysis are not well suited for a DOS approach since:1. They do not provide a nonobtrusive site for attachment to the solid-phase2. They are not condusive to wide structural variations (diversity)
M
M
PhPh
PhPh
NO
R R'
OR''
Mlinker1 linker2
aminoacid NN
R R'
OR''
M
tridentate Schiffbase complex
biasing elementto bind metals
diversity by varyingR, R', R'', linkers and amino acid
Metal-binding library planeasily varied structure;high yielding synthesis
NH
HN
NH
NH
O
O
R1 O
N
R3
HO
R2
R2
5NH
HN
NH
NH
O
O
R1 O
NH2
R2
R2
5
NH
HN
NH
O
O
O
R1 O
5
NO2
NH
HN
NH2
O
O
R1
5
R4
NH
NH2
O
5
NHFmoc
O
R1
HO
HBTU, HOBT,iPr2NEt, DMF
1.
2. 30% piperidine
O
ONO2
Cl
iPr2NEt, CH2Cl2-THF
H2N
NH2
R2
R2
Et3N, DMF
CHO
R3
HO
R4
DMF
NN
N
ONMe2
NMe2
PF6
NN
N
OH
HOBT =HBTU =
Parallel Synthesis of Schiff-Base Ligands on the Solid-Phase
H
N
CN
NF3C
O
HCN
1. catalyst2. TFAA
+ *
NH
HN
NH
NH
O
O
O
N
tBu tBu
HO
R2
R2 None Ti Mn Fe Ru Co Cu Zn Gd Nd Yb Eu
19 4 5 10 13 0 9 1 2 3 0 559 30 61 69 63 68 55 91 95 84 94 34
eeconversion
metal
Library 1
library size = 12 compounds
5
Although the library was based upon a Schiff base that would bind metals,the most enantioselective catalyst is the metal-free ligand!
Library #2: Screen metal-free ligand but vary amino acid, diamine, and salicyaldehyde
Initial Screening Identifies a Metal-Free Catalyst
Synthesis and Screening of Metal-Free Catalysts
NH
HN
NH
NH
O
O
R1 O
N
HO
R2
R2
Library 2
library size = 48 compounds (6 salicylaldehydes x 4 amino acids x 2 diamines): made in 48 flasks simultaneously-parallel diversity-oriented synthesis
5
R3 R4
A tBu tBuB tBu HC H tBuD tBu OMeE Br BrF tBu NO2
R3 R4
H2N
H2N
Ph
Ph
H2N
H2N
Leu, D-LeuHis, Phg (phenyl glycine)
R1-amino acids
R2-diamines
R3-salicylaldehydes
NH
HN
NH
NH
O
O
O
N
HO
5
tBu R4
test all 48 compounds in individual Strecker reactions
32% ee
R4 = tBu, H, or OMe
5% ee if D-Leu
HN
NH
NH
O
O
N
HO
tBu tBu
30-45%ee
better ee without linker
HN
NH
NH
O
S
N
HO
tBu tBu
45-55%ee
thiourea improves ee
if S = NH2, 21% ee
Winning Catalyst Would Not Have Been Found ByOne-At-A-Time Approach
Library 3
library size = 132 compounds (4 salicylaldehydes x 11 amino acids x 3 diamines): made in 132 flasks simultaneously-parallel diversity-oriented synthesis
H2N
H2N
Ph
Ph
H2N
H2N
Leu, Ile, Met, PheTyr (OtBu), Val, Thr, (OtBu),
Nor (norleucine), PhgChg (cyclohexylglycine,
t-Leu (tert-Leucine)
R1-amino acids R2-diamines X-salicylaldehydesHN
NH
NH
O
R1 S
N
HO
tBu X
R2R2
N
H2N
H2N Ph
OMeHtBuBr
HN
NH
NH
O
S
N
HO
tBu OMe
Ph
Winning Catalyst
t-Le
u
IleVal
Chg
Nor
Leu
Tyr
Met
PheThr
Phg
CH
OM
e
CH
H
CH
Br
CH
t-B
u
DP
OM
e
DP
H
DP
Br
DP
t-B
u
CP
OM
e
CP
H
CP
Br
CP
t-B
u
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
AParallel Combinatorial ApproachtoCatalyst Optimization
Amino AcidDiamine/Aldehyde
ee
MS Sigman, EN JacobsenJACS 1998, 120, 4901
NMR Solution Structure of the Optimized Strecker Catalyst
N
HO
t-Bu
OCOt-Bu
NH
HN
O O
HN Ph
t-Bu
EN Jacobsen and N Zondlo
NMR Solution Structure of the Imine-Catalyst Complex
H
N
HN
NH
NH
O
S
N
HO
tBu O
Ph
tBu
OR H
N
Ror
R = wide range of aromaticand aliphatic groups
HCN, PhCH3, -70ÞC
2 mol%
then TFAACN
NF3C
O
R CN
NF3C
O
R
or
77-95% ee70-98% yield
M. Sigman, P. Vachl, and E. N. Jacobsen Angew. Chem. Int. Ed. Engl. 2000, 39, 1279.
CN
N PhH
O
CO2H
N PhH
O
65% H2SO4, 45ÞC
CO2H
NH2 HCl1. HCl (conc.)2. H2, Pd/C, MeOH
99% ee84% y.
Enantioselective Synthesis of α-Amino Acids
Catalytic Enantioselective Synthesis of Quaternary Centers
P. Vachl, and E. N. Jacobsen Org Lett. 2000, 2, 867.
Me
N
RCNR
HNMe
R = aromatic and some aliphatic groups
HN
NH
NH
O
O
N
HO
tBu O
Ph
tBu
O2 mol%
HCN, PhCH 3, -70oC
500 µm PS bead
NH
O
O
SiO
i-Pr i-Pr
OHO
500 µm PS bead
NH
O
O
SiO
i-Pr i-Pr
OHO
Me
500 µm PS bead
NH
O
O
SiO
i-Pr i-Pr
OHO
O
OH OH
SR2
R1
O
OH OH
NR2
R1
R2SH or R2NHiPrOH, iPr2NEt
50ÞC
pool thensplit into 30 vials
(each vial containsequal amounts of the
three epoxyols)
90 diols;30 reactions
react with 30different 2Þ amines
or thiols
Split-Mix Diversity-Oriented Synthesis of a 1,3-Dioxane Library
S. Sternson, J. Louca, J. Wong, S. Schreiber JACS 2001, 123, 1740.
Building Blocks Used in the 1,3-Dioxane Library
HO
O HO
HO
O HO
HO
O HO
M e(±)
(±)
HN
M eHS
OH
HN
OH
NN
HN
SH
HN
HON SH
HNN
N
N
NHS
M e
N
HN
SH
H 2N
OH
SH
N + SH
O -N
N
SMe
SH
N
HNCl
ClN
NH
HNO
O
CO OH
SH
N SH
OH
O
HN
N N
N
HN
M e
M e
OH
SH
HN
HO NH
OH
NH
M eO OM e
NN
N N
SH
OH
M e
HN
NNH
ONH
M eNH
N
H N
O
N
O
SH
NH
O
O
O
O
O
HN
Cl
O H
(a )
(b )
M e
O
M e
O
O O
SR2
R1
O
O O
NR2
R1
NH2
NH2
O
O O
SR2
R1
NH2
O
O O
NR2
R1
NH2O
OH OH
SR2
R1
O
OH OH
NR2
R1
90 diols;30 reactions
MeO OMe
NHFmoc
MeO OMe
NHFmoc
or
HCl, TMSCl
then
N
O
H
pool, then splitinto 2 vials (90 diolsin each of 2 vials)
180 diols;32 reactions
Mereact with 2
different acetals
R1 = H oror
Split-Pool Diversity-Oriented Synthesis of a 1,3-Dioxane Library
S. Sternson, J. Louca, J. Wong, S. Schreiber JACS 2001, 123, 1740.
O
O O
SR2
R1
O
O O
NR2
R1
NH2
NH2
O
O O
SR2
R1
NH2
O
O O
NR2
R1
NH2
O
O O
SR2
R1
O
O O
NR2
R1
HN
HN
O
O O
SR2
R1
HN
O
O O
NR2
R1
HN
R3
O
R3
O
R3
R3
O
O
Cl R3
O
DMAP
pool, then splitinto 10 vials (180 differentdioxolanes in each vial);
add 1 of 10 acid chloridesto each vial
1800 compounds;42 reactions
1800 dioxolanes + 90 diols = 1890 different small molecules from 42 reactions
Split-Pool Diversity-Oriented Synthesis of a 1,3-Dioxane Library
S. Sternson, J. Louca, J. Wong, S. Schreiber JACS 2001, 123, 1740.
Building Blocks Used in the 1,3-Dioxane Library
M eO
M eO
NHFm oc
M eO
M eO
NH Fmoc
M e N C OCl
O
O
O
M e
NCO
M e
O
SC l
O O
OC l
O O
O
N
SC l
O
O
M e
O
N CO
Cl
O
M e
NH
Cl
O
SO O
M e
O N C S
O
O
M e
O O M e
O
O
M e
O
M e
O
(c )
(d )
O
O O
SR2
R1
O
O O
NR2
R1
HN
HN
O
O O
SR2
R1
HN
O
O O
NR2
R1
HN
R3
O
R3
O
R3
R3
O
O
1890 compounds;each bead containsone type of molecule
place each bead in aseparate well of a 384-well
plate
HF-PyridineHO
O O
NR2
R1
HN
HO
O O
SR2
R1
HN R3
O
R3
O
HO
O O
SR2
R1
HN
HO
O O
NR2
R1
HNR3
O
R3
O
1890 stock solutionsin 7μl of DMSO
Split-Pool Diversity-Oriented Synthesis of a 1,3-Dioxane Library
S. Sternson, J. Louca, J. Wong, S. Schreiber JACS 2001, 123, 1740.
Screening an Unbiased DOS Library Uncovers New Molecules to Explore Biology
S. Sternson, J. Louca, J. Wong, S. Schreiber JACS 2001, 123, 1740.
P. Hergenrother; K. Depew; S. L. Schreiber, J. Am. Chem. Soc. 2000, 122, 7849-7850.
Binding assay: 1. Activation of Glass Slides
Si Si SiO O
Cl Cl Cl
Si Si SiO O
Cl Cl Cl
Sii-Pri-Pr
ORSi
i-Pri-Pr
OR
Si Si SiO O
OH OH OH
Si Si SiO O
OH OH OH
THF, 4hTHF, 4h
Si Si SiO O
O O O
R R R
Si Si SiO O
O O O
R R R
glassslides
1% SOCl20.1% DMF
H2SO4H2O2
("piranha")
~12 h
HF•Py/THF; then TMSOMe
HO-R; add DMF
glassslides
1% SOCl20.1% DMF
H2SO4H2O2
("piranha")
~12 h
HF•Py/THF; then TMSOMe
HO-R; add DMF
Small Molecule microarraying robot
Biomimetic Diversity oriented Synthesis
Combinatorial chemistry is mainly used for optimization
N
NO
R4
HO
R2
R1
R3N
NO
Me
Cl
valium-a benzodiazepinthat binds to the GABA
receptor
ONHO
O
R2
R1O
OHO2C
Fmoc
NH2
EDCI, HOBt
OFmocHNR2
R1O
HMP
1. piperidine
2.O
FR3
NHFmoc
O
NH
R3
NHFmoc
OR2
O
R1
HMP
1. piperidine
2. AcOHN
HN
O
O
R2
R1
R3
HMPN
NO
O
R2
R1
R3
HMP
R4
ON
Bn
OLi
, R4X
N
NO
HO
R2
R1
R3
R4
TFA
B. Bunin and J. Ellman J. Am. Chem. Soc. 1992, 114, 10997.85-95% yield
benzodiazepin-basedlibrary design
N
NH
HN
O
Me Me
Me
OH
N
NH
HN
O
R1 OH
R3 O
R2
NH2
NH
CbzHN
OH
HN
NH
HN
O
R1 OH
HN
NH
HN
O
R1 O
O
O
O
N
NH
HN
O
R1 O
O
O
O
R2
R3
N
NH
HN
O
R1 OH
R2
R3 O
TfO
R1
O
OBn
2,6-lutidine
1.
2. H2, Pd/C, H+
3. TBTU, HOBT
O CO2Bn
Cl
polystyrene
1. , HCl
2. H2, Pd/C, H+
3.
1. R2CHO, NaBH(OAc)3,DMF-AcOH2. I2, pyridine
3. PdCl2(PPh3)2, CuI
R3
TFA-H2O
Indolactam V-a PKC activator Library based upon
indolactam
31-membered library:no improved PKC activator found
H. Waldmann et al. Angew. Chem. Int. Ed. Engl. 1999, 38, 2902.
Combinatorial chemistry library of natural products analogs
Natural products as reagents to explore biology
CH3O
CH3O
CH3O
OCH3
O
NH
Me
O
colchicine
colchicine altersmicrotubule dynamics
colchicine is usedto discover tubulin
O
H
HOH
HOO
Me
brefeldin A
brefeldin reversibly blocks protein
secretion by disruptinggolgi structure
Amaryllidaceae Alkaloids: Divergent Biosyntheses and Diverse Biological Activities
D. H. R. Barton and T. Cohen Festschrift A. Stoll; Birkhauser, Basel, 1957.
RO
RO
N
HO
R
OH
NR
O
RON
H
H
OH
HO
RO
RO
N
RO
RO
OH
O
NRH
OH
RO
RO
lycorinesgalanthamines
crinines
norbelladine
pretazettines
H
(antimalarial)
(antiviral)
(acetylcholineesterase inhibitor)
(Inhibits Cell Divisionin Yeast)enzyme-mediated
cyclizations
Biomimetic Diversity oriented synthesis
N
O
Me
OH
galanthamine
MeO
N
MeOHO
OH
H
NPO
BrPO
OH
OH
OO
P
N
O
HO
BrO
H
OH
1
Biosynthesis
Biomimetic Diversity-OrientedSynthesis
norbelladine
enzymes
bead 3
24
natural selection
cell-basedscreens
protein bindingscreens
Synthesis of natural product analogs
to optimize drug-likeproperties
Discovery of galanthamine-like
molecules withbiological propertiesbeyond those of the
natural productefficient synthesis ofthousands of natural
product-like molecules
Biomimetic Diversity oriented synthesis
NH
MeO
OH
OH
NH
MeO
O
OH
NH
MeO
O
O
4'-O-Methylnorbelladine Spiro-dienone
N-Demethylnarwedine
NMe
MeO
OH
O
Galanthamine
NO
BrO
Alloc
OH
H
OSi
iPr iPrN
O
O
BrO
Alloc
O3NH
O
HO
BrO
HO
HPhI(OAc)2
NorbelladineEquivalent
Spiro-dienoneNarwedineEquivalent
Pd(PPh3)4
morpholine
Biosynthesis
Biomimetic solid-phase synthesis
Add BuildingBlocks
P-450 likeenzyme cyclize
(CF3)2CHOHCH2Cl2
500μMpolystyrene
Biomimetic Diversity oriented synthesis
Diversity-Generating Reactions
NHO
BrO
O
H
OSi
iPr iPr3
H
R1OHPPh3,DIAD
NO
BrO
O
H
OSi
iPr iPr3
H
R1
NO
BrO
O
H
OSi
iPr iPr3
H
R1
R2SH, nBuLi
SR2
R3CHO, NaCNBH3or R3COCl;
R3NCO Acylation
NO
BrO
O
H
OSi
iPr iPr3
R3
R1
SR2
H2N OR4, orH2NNHSO2R4
NO
BrO
N
H
OSi
iPr iPr3
R3
R1
SR2
R4
>80%purity
>80% purity
>80% purity
>80% purity
norbelladine equivalent
NO
BrO
OH
OH
OO
CHOO
BrO
H2N
OH
HO
3
Si
Q
iPr
iPr
3
Si
Q
iPr
iPr
1. CH(OCH3)3, CH2Cl2wash, then NaBH3CN, AcOHMeOH-THF, 23ÞC
2. Cl O
O
iPr2EtN, CH2Cl2, 23ÞC
from tryosine
NH
MeO
OH
OH
4'-O-Methyl norbelladine
Q 500-600 micron1% DVB polystyrene
=
Nature’s startingmaterial for galanthaminebiosynthesis
Reductive amination of a tyrosine-derived amine prepares a norbelladine-like starting material on the solid-phase
Pelish, Westwood, Feng, Kirchhausen, Shair, J. Am. Chem. Soc. 2001, 123, 6740-6741.
First Step of the Galanthamine-Based Library
The oxidant PhI(OAc)2 promotes a biomimetic oxidative intramolecular biarylcoupling reaction to generate a seven-membered ring
NO
BrO
OH
OH
OO
Si iPr
iPr
N
O
O
BrO
OH
OO
Si iPr
iPr
NO
BrO
O
OH
OO
Si iPr
iPr
I
Ph
OAc
NH
MeO
OH
OH
NH
MeO
O
OH
Q
Q
Qnorbelladine equivalent
3 3
PhI(OAc)2,(CF3)2CHOH-CH2Cl2,
23ÞC
3
-2AcOH-PhI
4'-O-Methylnorbelladine Spiro-dienone
P-450 likeenzyme
Solid-Phase Biomimetic Oxidative Cyclization
Pd-catalyzed triple deprotection yields a bisphenol which adds selectively to one of the two diastereotopic enones. The stereochemistry is controlled by a remote stereogenic center.
N
O
O
BrO
OH
N
O
HO
BrO
H
OH
OO 3
Si iPr
iPr
3
Si iPr
iPr
Pd(PPh3)4 morpholine-THF23ÞC
prochiral carbon
diastereotopicenones
what is the mechanism of this reaction?how do you account for the stereoselectivity?
NH
MeO
O
OH
NH
MeO
O
O
Spiro-dienoneN-Demethylnarwedine
cyclize
Q Q
Deprotection initiates a stereoselective biomimetic cyclization
Mitsunobu coupling of the solid-phase phenol with five alcohols and a “skip”. The skip refers to a flask where no building block is added so that the phenol is represented in the library
The First Diversification Reaction: A Mitsunobu Reaction
N
O
HO
BrO
H
OH
Si iPr
iPr
N
O
O
BrO
H
R1O
H
Si iPr
iPr
N NCO2
iPr
iPrO2C
OH OH
NO2
O OHOH
Q
OH
Q3 3
R1OH, PPh3THF, 0
oC (2X)
Skip
building blocks that gave>80% yield were used
HN N
H
CO2iPr
iPrO2Cand Ph3P=OBy products:
A diastereoselective conjugate addition is achieved with seven thiolates and a skip so that the enone is represented in the library
N
O
O
BrO
H
R1O
H
N
O
O
BrO
SR2
H
R1O
H
3
Si iPr
iPr
3
Si iPr
iPr
R2SH, 2,6-lutidinenBuLi, THF 0ÞC
HS CF3
OMe
HSHS HS
HS HS OTBS
OHS Skip
building blocks thatgave >80% yield
Q Q
The Second Diversification Reaction: Conjugate Addition
An example of functional group diversification - introducing different types of building blocks at a single position, leading to diverse functional groups
A library with diverse functionality has diverse properties: in this case amides, ureas, and amines leads to library members which are charged or uncharged at physiological pH
N
O
O
BrO
SR2
H
R1O
H
N
O
O
BrO
SR2
R3
R1O
H
3
Si iPr
iPr
3
Si iPr
iPr
R3CHO, AcOH, MeOH-THF, then NaBH3CN in MeOH, 23ÞC or R3COCl, 2,6-lutidine, CH2Cl2, 23ÞC
or R3NCO, CH2Cl2, 23ÞC.
O
SO
OCNOCN
SMe
Skip
H
O
H
O
ClCl
O
H
N
O
O
BrO
SR2
R1O
H
3
Si iPr
iPr
EtHNO
N
O
O
BrO
SR2
R1O
H
3
Si iPr
iPr
N
O
O
BrO
SR2
R1O
H
3
Si iPr
iPr
uncharged at pH= 7.4 charged at pH= 7.4
H HH
charged at pH= 7.4
building block diversity
Q Q
Q Q Q
The Third Diversification Reaction: Acylation and Reductive Amination
The ketone is transformed - with functional group diversification - into oximes, hydrazones, and a ketone (via skip)
N
O
O
BrO
SR2
R3
R1O
H
Si iPr
iPr
N
N
O
BrO
SR2
R4
R3
R1O
X
H
SNH
O OH2N
SO
O
NMe2
NH
NH2
NH2
MeONH2
BnO
OMe
SNH
O OH2N
O2N
NH
NH2
Q
NH2O
O
HO
Si
iPr iPrQ
3
X =
X = H3
R4NH2, AcOH-MeOH-CH2Cl2,
23ÞC.
HF-pyridine, THF, 23ÞC then TMSOMe
Skip
building blocks thatgave >80% yield
The Fourth Diversification Reaction
Synthesis of a 2946 Member Library
OH
HSCF3
OMe
HS
HS
HS
HS HS OTBS
OHS
Skip Codon
Skip Codon
OH
NO2
O OH
OH
O
SO
OCNOCN
SMe
Skip Codon
Skip Codon
SNH
O O
SO
O
NMe2
NH2
MeONH2
BnO
OMe
SNH
O O
O2N
HN
NH2O
O
HO
NO
BrO
N
H
OR
R3
R1
SR2
R4
OH
H
H2N
NH2
H2N
O
H
O
ClCl
O
H
HN
NH2
Synthesis of a 2946 Member Library
Library synthesized as one type of compound per 500 micron bead
Library contains one type of core structure with various appendages.
A challenge is a library with diverse core structures.
OH
HSCF3
OMe
HS
HS
HS
HS HS OTBS
OHS
Skip
Skip
OH
NO2
O OH
OH
O
SO
OCNOCN
SMe
Skip
Skip
SNH
O O
SO
O
NMe2
NH2
MeONH2
BnO
OMe
SNH
O O
O2N
HN
NH2O
O
HO
NO
BrO
N
H
OR
R3
R1
SR2
R4
OH
H
H2N
NH2
H2N
O
H
O
ClCl
O
H
HN
NH2
Single beads are arrayed in each well of a 384-well plate, 18 total plates. Then, the compounds are cleaved simultaniously with HF-pyridine and re-suspended in DMSO to make 2946 stock solutions
384 Well Plate, ~50 nmol/well,6.7 uL DMSO/well, ~7.5 mM/well
N
N
HO
Br
O
HOH
H S
H
N
N
O
Br
O
HOH
H S
H
03B02O3B14
NO203K05O3K17
Plate 03
HNS
O
O
O
N
N
O
Br
O
HOH
H S
HOH
HNS
O
ON
N
N
O
Br
O
HOH
H S
H
OOMe
O
Assay of a 2946 member library
After cleavage from the solid phase, the solutions of library members are transferred using a robotic pin transfer arrayer.
Assay of a 2946 member library
Biochemical pathway
The Secretory pathway is responsible for the transport of newly synthesized proteins from the ER, through the Golgi to either the plasma membrane for secretion or to other cellular compartments
Olkkonen, V.M. et al. New Eng. J. of Med., 2000, 343, 1095.
ER Golgi Plasma Membrane
A GFP is used to screen for exocytosis
plasmamembrane
Golgi
ER
ER Block Golgi Block Control
14 Molecules 117 Molecules
O N
O
O
SBr
NO2
OH O N
OH
O
O
SBr
O
S
OH
Screen of the library at ~7.5mM revealed ER blockers and Golgi blockers
secramine
NO
BrO
N
HH
S
O
OH
OMe
golgiplasmamembrane
2μM
washing out secraminerestarts trafficking-reversible inhibitor
Pelish, H.E.; Westwood, N.; Feng, Y.; Kirchhausen, T.; Shair, M. D. J. Am. Chem. Soc. 2001, 123, 6740-6741.
Active compound identified
V. Diversity Oriented Synthesis – more examples
Shikimic acid library
– DOS based upon a complexity-generating reaction (reaction-based)
– Synthesis of a 2.1 million member natural product-like library
– Reaction selection and building block evaluation in DOS
– Quality control in DOS
O
NH
O
O
O
HN
NHR5
HOR6
O
R4
Reaction Based Library
V. Diversity Oriented Synthesis – more examples
Benzopyran library
– DOS based upon privileged structure - the benzopyran core
– Scaffold formation during attachment and cleavage
– Directed sorting in library synthesis
– The IRORI NanoKan system
– Further diversification of a library after cleavage
O
O
O
MeO
MeO
O
Me
Me
H
H
Privileged StructureBased Library
O. Tamura et al. Tetrahedron 1995, 51, 107
• A tandem esterification-[3+2] dipolar cycloaddition reaction gives a complex tricyclic structure, forming 3 bonds, 2 rings, and 3 new stereocenters in high yield and with complete stereocontrol
• The efficiency of this transformation and the complexity of the product make this reaction a good candidate for the basis of a library
HO O
MeON
O O
N
O
O
O
H
N O
O H
H O ON
O
H H
H
H
0.1 eq TiCl44Å MS
DCE, rt, 19h97%
+
A DOS Library Inspired by a Powerful Complexity-Generating Reaction
Testing of the Reaction on the Solid Support
• The model tandem reaction was tested on beads, and proceeded successfully with modified conditions
HO
H2N
OH
O
PyBOP, NMP
rt>98%
HONH
OO
MeONO
(SCNBu2Sn)2O4Å MS, tol, rt, 12h
>98%
O ON
O
H H
H
H
HN
O
H2N
O
O2N O
HN O
PSGeysen Linker (cleave with hν)
Caproic Acid Tentagel resin
H2N
+
The shikimic acid pathway converts simple carbohydrate precursors derived from glycolysis and the pentose phosphate pathway to the aromatic amino acids (Hermann and Weaver, 1999). One of the pathway intermediates is shikimic acid, which has given its name to this whole sequence of reactions. The well-known, broad-spectrum herbicide glyphosate (available commercially as Roundup) kills plants by blocking a step in this pathway. The shikimic acid pathway is present in plants, fungi, and bacteria but is not found in animals. Animals have no way to synthesize the three aromatic amino acids—phenylalanine, tyrosine, and tryptophan—which are therefore essential nutrients in animal diets.
Chiral Template for Library Synthesis
• The starting material for the library was made from (-)-Shikimic Acid:
– Source of chirality (both enantiomers were synthesized)
– Provides functional groups for additional building block diversification
H. B. Wood et al. J. Am. Chem. Soc. 1990, 112, 8907
OMe
O
HO
HO
OH
methyl shikimate
OH
O
HO
O(–)
Br
O
O
O OMe
O
Br
OH
AcO
OMe
O
O
HOLiOH
THF/H2O
0°C, 1 h
62%
1) NaOMe, MeOH
0°C, 30 min
2) NaOMe, MeOH
50°C, 10 min, 60%
CH3CN, 0°C
90 min, 76%
Amberlite–IR120
MeOH, 65°C
18 h, 100%
OH
O
HO
HO
OH
(-) shikimic acid
Chiral Template for Library Synthesis
• The synthesis of the (+) enantiomer of the starting material also proceeded from (-)-Shikimic Acid
OMe
O
HO
HO
OH
(–)-shikimic acid
Amberlite–IR120
MeOH, 65°C
18 h, 100%methyl shikimate
OH
O
HO
HO
OH
OH
O
HO
O(+)
OMe
O
HO
O
O
BzO
O
OMe
BzOH, DEAD
PPh3, THF
0°C → rt, 12 h
88%
LiOH
THF/H2O
0°C, 1 h
59%
DEAD, PPh3
toluene, 111°C
90 min, 96%
Reaction With the Chiral Template - Scaffold Synthesis
• Synthesis of the full scaffold on the solid phase was achieved with high efficiency
OH
O
HO
OH2N
NH
O
HO
O OO
HN
O ON
O
H H
H
+
PyBOP
DIPEA
NMP, rt, 1 h
>98%(+)PyBroP, DIPEA, DMAP
CH2Cl2, 0 °C → rt
3 x 3 h, >98%
HON
O OI I
OH
O
HO
OH2N
NH
O
HO
O OO
HN
O ON
O
H H
HPyBOP
DIPEA
NMP, rt, 1 h
>98%PyBroP, DIPEA, DMAP
CH2Cl2, 0 °C → rt
3 x 3 h, >98%
HON
O OI I
(-)
+
S. L. Schreiber et al. J. Am. Chem. Soc. 1999, 121, 9073
Diversification Potential of the Scaffold
• The scaffold offers many potential sites for elaboration and diversification, but they must first be experimentally tested
• Black arrows are transformations that were found to be experimentally viable
OO
HN
O O
N
O
H H
H I
nucleophilicaddition toepoxide
electrophilic capping of C5 alcohol
electrophilic capping of C6 alcohol
nucleophilicaddition to
lactone
Palladium catalyzedcoupling reactions
N-O bond reduction
electrophilic capping of
amine
Reaction Selection
• Requirements for a good library reaction:
– High yield
– High purity (chemo-, diastereo-, regioselectivity)
– High conversion
– Solubility of reagents in solvents compatible with solid-phase synthesis
– Reaction conditions compatible with solid-phase synthesis
• Avoid: pressure, extreme temperature, light- and moisture-sensitivity, conditions that may break beads
– Compatibility with linker used for library synthesis
– If split-pool synthesis is used, the scope of the reaction is important: the reaction should not be sensitive to sterics or the presence of any functional group used in the library
Examples of Reaction Evaluation
O ON
O
O
O
HN
H
H
H
nBuNH2
THF, rt.95%
Yb(OTf)3, PhCN
neat, rt, 16hlow yield
O ON
O
O
HN
H
H
H
HO
NH
Ph
O
O ON
O
O
O
HN
H
H
H
PhOCOCl
DIPEA, DCMrt, 16h, 50%
O ON
O
O
O
HN
H
H
H
OO
Ph
O ON
O
O
O
HN
H
H
H
ON
O
NH
O
HN
H
H
O
nBu
HO
Ritter reaction:
Debenzylation/Carbamateformation:
Aminolysisof the lactone:
all reactions proceed in low yield
Diversification Sequence Development
• Attempted reactions with the amide were uniformly unsuccessful
OO
HN
O ON
O
H H
HI
OO
HN
ON
H
HO
O
NH I
NH
O
O
HO
OO
HN
ON
H
HO
O
NH
OO
HN
ON
H
HO
O
NH
OO
HN
ON
H
HO
O
NH
OH
PhB(OH)2
Bu3SnOH
Pd2(dba)3, AsPh3NMP, rt, 30h
Pd(PPh3)4, DMFDIPEA, rt, 30h
(Ph3P)2PdCl2CuI, DIPEADMF, rt, 30h
nBuNH2
THF, rt, 24h>95% conversion
+
Reversion !
Diversification Reaction Sequence and Building Block Testing
• Reversal of steps solved the problem
• Testing of building blocks was conducted on a representative route
O ON
O
O
O
HN
H
H
H
O ON
O
O
O
HN
H
H
H
I
(Ph3P)2PdCl2CuI, DIPEA
DMF, rt, 2 h
>95%
ON
OO
HN
H
HHO
O
NH
MeO
2-pyridinol
THF, rt, 16 h
>95%
H2N
OMe
ON
OO
HN
H
HO
O
NH
MeO
(EtCO)2O
2,6-lutidineDMAP, DCM
95% OEt
O ON
O
O
O
HN
H
H
H
(Ph3P)2PdCl2CuI, DIPEA
DMF, rt, 2 h
Test 50alkynes
Choose 30
R
ON
OO
HN
H
HHO
O
NHR
2-pyridinol
THF, rt, 16 hTest 87amines
Choose 62
ON
OO
HN
H
HO
O
NH
MeO
Test 98acids
Choose 62
DIPC, DMAP
CH2Cl2, rt, 16 h
R
O
Pathway Development
Building Block Testing
OMe CN
H2N H2NOMe
H2N H2N H2N N
OH2N
H2N
OMe
OMe
HO
O
HO
O
OMeHO
O
HO
O
HO
O
NHO
OOMe
HO
O
OMe
O
SKIP
SKIP
SKIP
1
8
2 3 4 5 6 7 8
1 2 3 4 5 6 7 8
1 2 3 4 5 6 7
LC–MS analysis of 8 pools of 64 distinct compounds – 456 of 456 compounds detected
Atmospheric Pressure Chemical IonizationPool 4
Synthesis and Analysis of a Small Test Library
hν (365 nm)photocleavage
photocleavablelinker
CAN oxidativecleavage
binary encoding tagstructure elucidationby EC-GC analysis
of binary code
chemical genetic assayswith engineered cells
in nanowells
90 μm TentaGelcopolymer bead
librarycompound
Ph
Ph
Ph
O
OMe
O O
OO
NH
O
NH
NO2O
Xn( )m
50
Choosing An Encoding Strategy and Linker
Synthesis of the Complete Library
NH
O
O
HO
O ON
O
O
O
HN
H
H
H
I
O ON
O
O
O
HN
H
H
H
R4
ON
OO
HN
H
H
O
NHR5
HO
ON
OO
HN
H
R4H
O
NHR5
OR6
O
H2N NH
O
H2N
6 compounds
3 iodobenzylnitrones
18 compounds
30 alkynes+ skip
558 compounds
35,154 compounds
62 acids+ skip
2,180,106 compounds
62 amines+ skip
2 spacers+ skip
2 epoxycyclohexenolenantiomers
3 compoundsTentaGel withGeysen linker
R4
( )n98% >98%
>98% 90 – 95%
95 – >98% 95 – >98%
ON
H
O
O
O
HN
NHR5
HOR6
O
R4 F
H2NH2N
OH2NH2N
O
O
NH2N
H2N
OH2NH2N O
O
NH2N
ON
H2N
OH2N
H2N
H H2NH2N H2N
H2N
H2N
MeO
H2NNO2
H2N H2N
NH2N
NH2N
H2NF
HO
O
HO
O
HO
O
Cl
HO
O
HO
O
HO
O
HO
O
HO
O
HO
O
O
HO
O
OMe
O
HON
O OO
HOO
O
O
HO
O
MeO
O
HO
O
O
HO
O
O
OMe
FeHO
O
HO
O
HO
O
CN
HO
O
CNHO
O
OMe
O
OMeHO
O
HO
OOMe
HO
O
OMeHO
O
OMe
HO
O
OMe
HO
O
OMeHO
O
O
O
HO
O
MeO
O
N
HO
O
HO
O
N
N
NHO
O
NHO
O
N
HO
O
N N
O
O
N
CN
Cl
O O
O O
OO
MeO
OHMe
H
H H
OHOHOH
H2N
OH
H2NH2N
OH2N
H2N H2N
H2N N
H2N H2N H2N H2N
H2N
O
OSiH2NSiH2N
OMe
MeOOMe
H2N N N
O
OO
OOH2N
H2NH2N H2N
H2N
H2N
F
H2N
MeO
OMe
OMeH2N
H2N
O
O
OMe
OMeH2N
H2N
H2N
H2N
OMe
H2N
OMe
H2N OMe
H2N S
NH2NN
H2N
H2N
NH
SNH2
O O
H2N
H2NCF3
H2N
OCF3
H2N H2N
O
HO
O
HHO
O
HO
O
HO
O
HO
O
HOOMe
O
O
HO HO
O
HO
O
HO
O
HO
O
HO
O
OHO
O
O HO
O
HOO
O
HOO
O
HO
O
O
O
HO
O
NHO
O
SHO
O
HO
O
O
HO
O
O HO
O
SHO
O
S
CF3
HO
O
HO
O
CF3 HO
O
CF3
HO
O
N
NN
HO
OHO
O
O
2,180,106 compounds
S. L. Schreiber et al. J. Am. Chem. Soc. 1999, 121, 9073
Building Blocks Used in a 2.1 Million Member Library
Summary of Shikimic Acid Library Development
1. Identification of a complexity generated reaction
2. Testing and adopting the reaction to the solid
phase
3. Reaction pathway development
4. Building block testing
5. Quality control - Synthesis of a test library
6. Encoding
7. Library synthesisShikimic Acid Library
Reaction-Based
Split-Pool Synthesis
161 Reactions, 2.1 million compounds
Privileged Structure
• Privileged Structure: a structural pattern which is commonly found associated with a particular property and may contribute to that property
• Example: Biological Activity
– The benzodiazepine substructure is found in a wide variety of biologically active natural products
• Example: Asymmetric Catalysis
– The binapthyl substructure is part of many effective chiral ligands
PPh2
PPh2
OMe
PPh2
BINAPAsymmetric
hydrogenation
MOPEnantioselective hydrosilylation
OH
OH
BINOL
PPh2
OP
O
O
Asymmetric hydroformylation
N
N
MeO
Ph
N
NH
O Ph NO
N
HN
HO
H
HN
N
OH
Me
O
OHH
NH2
O
CyclopeninPhytotoxic
activity
AsperlicinHuman
Cholecystokinin antagonist
AnthramycinAntitumor and
antibiotic activity
OO O
OMe
MeOO
MeMe
H
H
O
O
O
Me
Me
HOOH
H
H
O
O
O
MeMe Me
Me
Me
OH
O
OMe
Me
R1
R2
R3
R4
deguelinelectron transport
inhibitor
daleformisICE inhibitor
calanolide AHIV RT inhibitor
Nicolaou et al. JACS, 2000, 122, 9939-9967 (3 full papers)
Benzopyran as Privileged Structure
• The benzopyran substructure is found in many diverse biologically active natural products
Benzopyrans: Privileged Structure?
Benzopyrans: Privileged Structure?
• Attachment to the solid phase and cyclization to the dihydrobenzopyran are accomplished simultaneously
• The selenide linker is stable to strong acidic, basic and reductive conditions (and some oxidants), but is cleaved with mild hydrogen peroxide treatment
• Cleavage of the compound from the solid support completes the benzopyranstructure
A Plan for a Library of Benzopyrans
Nicolaou et al. JACS, 2000, 122, 9939-9967 (3 full papers)
OHMe
Me
R1
R2
R3
R4
BrSe
OMe
Me
R5
R6
R7
R8
SeH2O2
OHMe
Me
R1
R2
R3
R4
Se
OMe
Me
R5
R6
R7
R8
Se
OH
Br-
OMe
Me
R5
R6
R7
R8
OMe
Me
R1
R2
R3
R4
Se
diversification
THF, 25ÞC
The First Diversification Pathway
• Addition of nucleophiles to an aldehyde scaffold was followed by acylationor Mitsunobu reaction of the resulting secondary alcohol
OMe
Me
Se
OMe
Me
Se
OMe
Me
Se
OMe
Me
Se
OMe
Me
OMe
Me
R2
R1
N
N
R2
R1
N
N
H
O
R1
R2
O
R1
O
R3
R2
OH
R1
R2
O
R1
O
R3
15O
R3Cl
Et3N,DMAP
20 R2MX
N
HN
8 R4
R4R4
THF, 0ÞC
Ph3P, DEAD,CH2Cl2, 25ÞC
H2O2, THF, 25ÞC
9 aldehydes
H2O2, THF, 25ÞC
OMe
Me
Se
OMe
Me
Se
OMe
Me
Se
OMe
Me
Se
OMe
Me
OMe
MeR1
N
R2
SO2R4
R1
N
R2
SO2R4
H
O
R1
R1
N
R2
R3
O
R1
NHR2
R1
N
R2
R3
O
15O
R3Cl
20 R2NH2
Et3N,DMAP
Et3N,DMAP
10
NaCNBH3,THF-MeOH, 0ÞC
H2O2, THF, 25ÞC
H2O2, THF, 25ÞCR4SO2Cl
The Second Diversification Pathway
• Reductive amination followed by acylation or sulfonylation of the resulting amine
9 aldehydes
OMe
Me
Se
OMe
Me
NC
NCO
MeMe
Se
NC
OMe
Me
Se
NC
OH
KOEt, THF, 25ÞC
OMe
Me
Se
NC
O O
H
O
R1
15R2
OOHN
CCl3R5
R2
R5
R2
R2
H2O2THF, 25ÞC
R2
9 aldehydes
BF3Et2O, CH2Cl24Å MS, 0ÞC
If R2 = p-OTHP cleave
R2 = OHTsOHTHF-MeOH
5 sugars
The Third Diversification Pathway
• Knoevenagel condensation of a benzylic nitrile was followed by cleavage of some library members - and glycosylation of library members containing a protected phenol
Building Blocks Used in the Benzopyran Library
Synthesis Scheme for the Entire Library
www.irori.com
The IRORI System: Kan Reactors for Solid Support
• The IRORI system carries each library member on beads contained in a plastic or ceramic capsule (“kan”)
• Kans have higher loading levels than beads, and are more mechanically robust
• Handling of the IRORI kans is highly automated
• Each Kan has a laser-readable tag
• The Kans can be read and sorted in a high-throughput machine
• Encoding of an IRORI library:
– The path of a Kan through the library synthesis is pre-determined
– At each step, the Kan is sorted into the appropriate reaction vessel by a computerized sorter (2,000 Kans/hour)
– At the end of the library synthesis, the path followed by each Kan is known by the computer, so no decoding of the library is necessary
www.irori.com
Individual Labeling of Kans Simplifies Decoding
IRORI Equipment for Synthesis of a Large Library
www.irori.com
Construction of the Library with IRORI
• Directed sorting of library members greatly simplifies the execution of a complex library synthesis plan
• Analogous to selective splitting of compounds in a split-pool library
OMe
Me
SeH
OHO
OMe
Me
Se
O
O
R2
OMe
Me
O
O
R2
OMe
Me
O
O
R2
O
OMe
Me
O
O
R2
OR3
OH
OMe
Me
O
O
R2
OR3
OAc
R1
O
R2
O
OMe
R1
R1R1
Ac2O
DMAP
DMAP
N
N
Me
O O
Me Me
R1
R1
piperidine, 95ÞC
R3OH
Amberlyst-15(H+)
=
H2O2, THF, 25ÞC
acetone
scavengerresin
Diversification After Cleavage from the Solid Phase
• The benzopyran library could be elaborated and further diversified after cleavage from the solid phase
OMe
Me
NS
O
O
OO
Benzopyran Library
Privileged Structure-Based
Directed Sorting
18 reactions, 10215 compounds
Benzopyran library
Microreactors in Chemical Synthesis
V. Excursion: New synthetic techniques in chemistry
Changes in the way we do chemistry
Chemical dimensions
Surface to volume ratio
Small dimensions = short mixing time
Small dimensions = short mixing time
Small dimensions = efficient heat transfer
Nu = Nusselt number; describesenhancement of heat transfer from a surface in a “real” situation if compared toconductive heat transfer.
Exact control of residence time
Safety
Small volumes and better control of reaction conditions reduce
risk and open new process windows (reactions at very high temp-
eratures and pressures with very short reaction times)
A Closer Look at Mixing
density x velocitykinematic viscosity
Reynolds number =
laminar < Re = 30 < turbulent
A Closer Look at Mixing
Induction of vortices (Strudel, Wirbel) by stirring, moving parts or structured channels
A Closer Look at Mixing
For all mixing techniques:
Microreactor apparatus set up
Microreactor apparatus set up
Inlet 1 Inlet 2
Outlet Outlet
Inlet
Microreactor apparatus set up
Microreactor apparatus set up
Microreactor apparatus set up
Microreactor apparatus set up
Microreactor apparatus set up
Microreactor apparatus set up
Microreactor apparatus set up
Lab scale reactions
Michael reaction
O O O
EtO
O O
O OEt
+iPr2EtN, EtOH
Synthesis of 1,3-Diketones
Synthesis of Tetracyclone
O
PhPh
O O
Ph Ph
O
Ph Ph
PhPh+
Base, ΔT
Butanol
70 - 800C
Mixing and reaction at +80oC:
Mixing and reaction at + 90oC:
Aromatic Nitration
Segmented flow
Landolt Reaction - Iodine Clock
IO3- + 6 H+ + 3 HSO3
- ———> I- + 3 HSO4- + 6 H+
IO3- + 6 H+ + 6 I- ———> 3 I2 + 3 H2O
Landolt Reaction - Iodine Clock
IO3- + 6 H+ + 3 HSO3
- ———> I- + 3 HSO4- + 6 H+
IO3- + 6 H+ + 6 I- ———> 3 I2 + 3 H2O
Segmented flow
Segmented flow
Controlled precipitationIn a bubble tube
Segmented flow
Micro-encapsulation of drugs in polymeric microspheres
Polylactic acid; polylactic-polyglycolic acid
Lab process for microsphere preparation:
Segmented flow
Micro-encapsulation of drugsMicro mixer process
Resorchin Azocoupling reaction
OH
OHNO2
N2
OH
OH
NN
NO2
BF4+
C6H6O2 C6H4BF4N3O2 C12H9N3O4
[Base NEt3]
low base concentration
high base concentration
Peptide Synthesis
(4{N-[1-(4,4-dimethyl-2,6-dioxocyclohexylidene)-3-methylbutyl]-amino} benzyl alcohol)= Dmab-OH
Peptide Synthesis
Suzuki coupling
Photo reactions
Combinatorial compound library synthesis
Domino reaction: Knoevenagel condensation andHetero-Diels-Alder
Combinatorial compound library synthesis
Amide formation and Knorr-Pyrrol Synthesis
Scale up
“Got a few problems going from lab scale up to full commercial scale”
Asymmetric synthesis via organoboranes
Asymmetric synthesis via organoboranes
Synthesis of the chiral allylboranes
Asymmetric synthesis via organoboranes
Synthesis of chiral allylalcoholes
Asymmetric synthesis via organoboranes
Synthesis of chiral allylalcoholes
Asymmetric synthesis via organoboranes
Azo pigment synthesis
Azo pigment synthesis
Azo pigment synthesis
10 t per year
Azo pigment synthesis
Advantages:
• Constant product properties compared to batch synthesis• Short development time (18 months) from lab to plant• Switching between products is fast• Low operating cost
Summary
Microreactor systems allow a better control of reaction conditionsand therefore provide advantages for• fast reactions• very exothermic reactions• handling of dangerous reaction intermediates• reactions at very high temperatures and pressures• sequential reactions
A better control of reaction conditions may reduce side reactions.
Optimization of reaction conditions is facilitated and the use of otherwise difficult accessible “process windows” becomes possible.
Simple scale up of a reaction by “numbering up”(parallel use of several microreactors)
Production of t/year in a laboratory environmentCustomized production on demand
Molecular Complexity
Defined by Our Intuition
– Complexity is defined in part by the frontiers of chemistry
– Complexity resists definition, but we know it when we see it
• Molecular Size
• Element and Functional Group content
• Cyclic Connectivity
• Stereocenter Content
• Chemical Reactivity
• Structural Instability
VI. Complexity Generating Reactions
Intuitive Definition of Complexity
• Contributors to Complexity
– Molecular Size
Palytoxin
• 115 carbon chain• 71 stereogenicelements• Requires 42 hydroxyl protecting groups!
• Contributors to Complexity
– Element and Functional Group Content
Vancomycin
Free Acid
Phenols
Carboxamide
Atropisomerism
Aminodisaccharide
Benzylicβ-hydroxyls
Intuitive Definition of Complexity
• Contributors to Complexity
– Cyclic Connectivity
– Stereocenter Content
Ginkgolide B
• 6 fused 5-membered rings• Dense functionality• 13 of 14 ring carbons are asymmetric
Intuitive Definition of Complexity
• Contributors to Complexity
– Chemical Reactivity: Neocarzinostatin Chromophore
OO
O
ORO
O
O
OH
H3C
OCH3
HSR1
OCH3
OHHO
MeHN
H B
RO
O
O
OH
H3C
OCH3
SR1
• •
OO
O
OHRO
O
O
OH
H3C
OCH3
SR1
OO
O
OH
R =
R = H
DNA-damaging agent
• Aglycon decomposes in 1-2 hours
Intuitive Definition of Complexity
• Contributors to Complexity
– Structural Instability
• Example: Phomoidride B (CP-263,114)
H
OO
O
HO2C
O
O
O
O
Free Acid
Sensitive pseudoester
Reactive maleicanhydride
Highly epimerization-sensitive
Intuitive Definition of Complexity
• Bertz, S. H. J. Am. Chem. Soc. 1981, 103, 3599-3601.• Using graph theory: Complexity (C) is related to the number of times (n)
a given pattern can be mapped onto the molecule
• These methods are limited to simple connectivity, double bonds, etc. Influence of stereochemistry, heteroatoms, functional groups, reactivity, and stability are not effectively included
A Computational Definition of Complexity?
pattern
Propane
Adjacent Bonds 43.0215.518.00
Atoms
Bonds
8.00 8.00
15.51 15.51
C(n) = 2n log2 n - Σni log2 nii
15.51 16.00
8.00 9.51
8.00 15.51 43.02 4.00
16.00
Symmetry reduces the complexity
The number of patterns
Why Complexity in DOS?
• Intuition and the desire to emulate nature
– Nature makes molecules of a wide range of complexity for a wide range of functions
OH
HOO
N
NH2Cl
H
N
N
H2N
OH
N
N
N
H2N
O
H
HH
H
H
OMe
Me
OH
MeO
OH
O
S
NMe
N
Me
NH H
ONH
ON
Me
NH
ON
Me
NH
O
H2N
NH
Epothilone BAnti-mitotic by stabilization
of microtubules
Palau'aminePotent immunosuppressant
by unknown mechanism
Distamycin AAntibiotic by binding to the
minor groove of DNA
KramerixinPotent, broad-spectrum
antifungal agent
Challenges of Complexity in DOS
• Length of the Synthetic Route
– Target-oriented synthesis of a complex natural product often requires 20-40 steps
– The length of a synthetic route on the solid phase is limited to 5-15 steps by purity considerations
Ginkgolide B
Corey et al. - 31 linear stepsJACS, 1988, 110, 649.
Crimmins et al. - 25 linear stepsJACS, 1999, 121, 10249.JACS, 2000, 122, 8453.
A B
10 steps
Avg. transformationefficiency
% of desired B onbead
80%90%95%
11%35%60%
?
Challenges of Complexity in DOS
• Planning a complex library requires reliable reactions
– Testing of reactions and building blocks is conducted in a “representative” route, but quality control of all reactions in a library synthesis is impractical
– Density of functional groups and steric crowding can cause unpredictable reactivity
• A complex library requires rapid generation of complexity to minimize the number of steps
Complexity-Generating Reactions
• Efficient and reliable complexity-generating reactions (CGRs) are necessary in DOS to assemble natural product-like molecular frameworks in few steps
• Reactions which rapidly create rings, stereocenters, carbon-carbon bonds, and functional groups
– Cycloaddition reactions
– Multicomponent couplings
– Tandem reactions - Two or more transformations conducted in sequence in one reaction vessel
• Tandem cascade reactions - no isolable intermediates
[4+2][4+2]CO2Me
CO2MeMeO2C CO2Me
+CO2Me
CO2Me
OH
H
H H
O OKH, heat
18-crown-6
hυ, heat
Types of Tandem Reactions
TMSO
[4+2] [4+2]
CO2Me MeO2C
O
CO2Me
Denmark, S. E.; Thorarensen, A. Chem. Rev. 1996, 96, 137-165.
Schreiber, S.L.; Santini, C. J. Am. Chem. Soc. 1984, 106, 4038.
• Tandem consecutive reactions - a change in conditions starts the subsequent
transformations
• Tandem sequential reactions - requires addition of another component
Design of Tandem Reactions
Thermodynamics
- Keep in mind that reactions must be energetically favorable
– The Benson additivity rules are useful for the quick calculation of the bond and ring strain energies gained and lost in a reaction
– The introduction of strain into a molecule is often an effectiveway of promoting rearrangements
C-CO-CN-CCl-CBr-CI-C
C-CC-OC-N
H-Csp3
H-Csp2
H-CspH-OH-O2CH-N
σ-bonds π-bonds
100103125102112103
858479827054
678875
Approximate Selected Energies (ΔH only)
3-C4-Cepox.
rings
282628
Design of Tandem Reactions
Kinetics
– Intramolecular reactions are greatly accelerated over an analogous intermolecular reaction
– Proximity can be used to enforce the desired reactivity
– Irreversible termination steps can be included if the product would otherwise be a small (uphill) component of an equilibrium
Design of Tandem Reactions
• Key elements
– Recognition of new reactive patterns in the products of a reaction
• “Programmed” starting materials
– Certain functional group patterns lead to cascade reactions
– e. g. spaced olefination: Heck, radical, cation cascades
Iradical
initiation
I
initiator + spaced radical acceptors
O
Br
OMe
O
O
OMe
O
Br
O
OOMe
-
base
Keying Elements: • Enolate • Leaving group
Brooking, P.; Crawshaw, M.; Hird, N. W.; Jones, C.; MacLachlan, W. S.; Readshaw, S. A.; Wilding, S. Synthesis 1999, 1986-1992.
Complexity-Generating Reactions in DOS
• Tsuge reaction followed by a [2,3]-dipolar nitrile oxide cycloaddition
NOH
Cl
R2
HN
O
O
O
N
Cl-
HN
O
O
ON
NO O
R1
HH
NO
H
H
R2
H
Et3N
N
O
O
R1
HN
O
O
ON
NO O
R1
HHH
R3HN
ON
NO O
R1
HH
NO
H
H
R2
HR3NH2
Complexity-Generating Reactions in DOS
• Tandem esterification - nitrone [3+2] cycloaddition approach to a tetracyclicscaffold
Tan, D. S.; Foley, M. A.; Shair, M. D.; Schreiber, S. L. J. Am. Chem. Soc. 1998, 120, 8565-8566.
O
O
NH
OO N
O
PyBroPor HATU
DMAPiPr2NEt
NO
HO
O
X
X
( )0,1
HO
O
NH
O
O
HN
O
O ON
O
H H
H
+
( )0,1
[3+2]
Kiselyov, A.S.; Armstrong R.W. Tetrahedron Lett. 1997, 38, 6163.
Complexity-Generating Reactions in DOS
• A three-component condensation gives tetrahydroquinolines from simple starting materials
O O
NH2 CHO
TFA
O O
N
H
H
O O
HN
H
H
O O
N
+ +
Complexity-Generating Reactions in DOS
• An oxidative coupling - hetero-Diels-Alder approach to Carpanone-like molecules
Lindsley, C. W.; Chan, L. K.; Goess, B. C.; Joseph, R.; Shair, M. D. J. Am. Chem. Soc.2000, 122, 422-423.
Chapman, O. L.; Engel, M. R.; Springer, J. P.; Clardy, J. C. J. Am. Chem. Soc. 1971, 93,6696.
OR3
HO
R4
O
O
R3O
R4
R1
R2
O
OOR3
R1R4
O
H
H
R2
ODiels-AlderHO
R1
O
R2
PhI(OAc)2+
OH
O
O
Me
OH
OO
Me
PdCl2
O
O
O
O
OO
MeMe
Diels-Alder
O
O OO
Me
Me
O
O
H
H
+
Carpanone
46%
Complexity-Generating Reactions in DOS
• A biomimetic oxidative phenolic coupling used to make a library of Galanthamine-like molecules
(a) Pelish, H. E.; Westwood, N. J.; Feng, Y.; Kirchhausen, T.; Shair, M. D. J. Am. Chem. Soc. 2001, 123, 6740-6741. (b) Kita, Y.; Arisawa, M.; Gyoten, M.; Nakajima, M.; Hamada, R.; Tohma, H.; Takada, T. J. Org. Chem. 1998, 63, 6625-6633.
Eichhorn, J.; Takada, T.; Kita, Y.; Zenk, M. H. Phytochemistry 1998, 49, 1037-1047.
OH
NH
OH
MeO
OH
NH
O
MeO
GalanthamineNorbelladine
enzymes
OH
N
O
Br
O
O O
O
O
NH
O
Br
HO
O
O
N
O
Br
O
O O
OPhI(OAc)2 Pd(PPh3)4
morpholine
Chen, S.; Janda, K. D. J. Am. Chem. Soc. 1997, 119, 8724-8725.
Complexity-Generating Reactions in DOS
• A sequential 1,4 cuprate addition - enolate alkylation approach to a library based on Prostaglandins
CO2MeTfO
OO O
O
Li2Cu(CN)Me2 OO O
OTMS
OTBS
MeLi;
OO O
O
OTBS
CO2Me
Bu3Sn
OTBS
1)
2) TMSCl
Tietze, L.F. Angew. Chem. Int. Ed. 1996, 35, 651.
Complexity-Generating Reactions in DOS
• A tandem Knoevenagel-Ene reaction gives complex cyclic compounds
O
O
OMeO
O( )n
O
O
OMeO
( )n
O
O
OMeO
( )n
RR
R
Paulvannan, K. Tetrahedron Lett. 1999, 40, 1851-1854.Lee, D.; Sello, J. K.; Schreiber, S. L. Org. Lett. 2000, 2, 709-712.
Complexity-Generating Reactions in DOS
• An Ugi - Diels-Alder sequence gives a complex tricyclic core from four simple components
ORN
O
HN OBr
OHN
OH
HH
OR
H2N
OOHC CN
HNHO2C
O
Br
SiO
OR
N
O
HN OBr
OHN
O
R =
Diels-Alder
,
Ugi 3-ComponentCoupling
Lee, D.; Sello, J. K.; Schreiber, S. L. Org. Lett. 2000, 2, 709-712.
Complexity-Generating Reactions in DOS
• The tricyclic core is subjected to an olefin metathesis cascade to give a rearranged tetracyclic core
ORN
O
HN O
OHN
OH
HH
Br
ORN
O
N O
Br
ON
OH
HH
N N
RuPh
PCy3ClCl
Br
KHMDS
N
N
N
OH H
OH
O
OH OH
Br
1)
2) HF•py
Tandem Cycloadditions and Sigmatropic Rearrangements
Tandem Cycloadditions and Sigmatropic Rearrangements
Radical cyclization
Heck Cascades
• Alkyne or 1,1-dialkylalkene groups are positioned three to five carbon apart leading to the formation of 5,6, and 7-membered rings
I
SiMe3
SiMe3
I
SiMe3
SiMe3
I
I
Zipper-mode
Dumbbell-mode
Spiro-mode
Linear fused-mode
Tandem Heck Reaction
• Intermolecular Heck reaction followed by intramolecular one
• Syn-Carbopalladation leads to only one geometric isomer
E. Negish. et al. J. Org. Chem. 1989, 54, 2507
Stable Organo-Pd intermediate
without syn β-H
Syn-carbopalladation
I
Me MeLnPd
MeLnPd
CO2Me
Me
MeO2C
3 mol %Pd(PPh3)4
2.5 eq. Et3N100 oC, 12 h
80 %
Tandem Heck Reaction
B. M. Trost et al. J. Am. Chem. Soc 1992, 114, 9836
• Intermolecular Heck reaction terminated with intramolecular one
Br
H
OH
TBSO OTBS
PdLn
TBSOOTBS
H
R
TBSO
H
PdLn
OTBS
H
R
LnPd
H
TBSO OTBS
R
H
TBSO OTBS
OH
Pd2(dba)3-CHCl330 % PPh3, Et3N
toluene52 %
Sequential Tandem Heck Reaction
L. Tietze et al. J. Am. Chem. Soc. 1998, 120, 8971
• Two Heck reactions are achieved in one-pot
H
OtBu
H
MeO
OtBu
Br H
PdP
OAc
R R
BrBr
OtBu
H
MeO
H
H
He
H
MeO
OtBu
H
H
LnPdHa He LnPd Ha
H
MeO
OtBu
H
120 oC
(R: o-tol)
10 %Pd(OAc)2,22 % PPh3,
60 oC, 60 h.CH3CN, DMFnBu4N(OAc)
2.0 eq
63 %
MoreReactive
Syn-carbopalladation
Syn- Elimination
LnPd
Stable Neopentyl Organo-Pd-intermediate
L. E. Overman et al J. Am. Chem. Soc. 1999, 121, 5467
• Strained tricyclic system
I OTBS
R H
Me
R
PdLn
HH
OTBS
R
OTBS
H
R
OTBS OTBS
R
H
LnPd
O
HOOBz
HO2C H
H
A
Scopadulic acid
10 %Pd(OAc)2, 20 %PPh3, Ag2CO3,THF, reflux
> 90 %
slowcyclization
Neopentyl-type
PdLn
Pd(0)
Chemistry of Stable Organo-Pd Intermediate
An Opportunity for Diversification
R3
R1R2R
R3
R1R2Nu
RNu
R3PdLn
R1R2
CO
R SnR'3R B(OH)2
R3R
R1 R2
R3
R1R2 O
PdLn
R3R
R1R2
Heck
Suzuki Coupling
Stille Coupling
Sequential Tandem Heck-Suzuki Reaction
• Three component coupling reaction on solid support
• Stoichiometric amount of Pd used
J. A. Ellman. et al J. Org. Chem. 1996, 61, 4494
X = 4-MeO
= 4-Me
= H
R = 4-MeOC6H4
= 4-MeC6H4
N
O
O O
TMS
N
O
O O
TMS
PdLn
X N
O
O O
TMS
R
X
Pd(PPh3)4
ArBr, THF66 oC
RB(OH)2
PPh3, Na2CO3
THF, 66 oC
H
without availablesyn-β-hygrogen
H
Heck-Carbonylation and intermolecular Nucleophilic addition
• Three component coupling reaction
F. Vöglte. et al “Stimulating concepts in Chemistry” pp 56
η3-allyl-Pd
N
I
SO2Ph
CO
H2N
HN
R
CONH2
O
NSO2Ph
PdLn'
CO
NSO2Ph
O
PdLn'
N
SO2Ph
NH2
N
SO2Ph
PdLn
N
SO2Ph
O
NH
HN
R
O
CONH2
NSO2Ph
PdLnPd(0)
Pd(0)
LnPd
R
Multicomponent Reactions
• Multicomponent reaction: A reaction in which three or more reagents react in one pot to generate a product containing atoms from all reagents.
R. Robinson J. Chem. Soc. 1917, 111, 762. B. Trost and A. Pinkerton JACS 1999, 121, 4068.
H2O, 25 ºC
CHO
CHO
H2N O
CO2H
CO2H
ON
CO2H
CO2H
CaCO3
AcO
OO
OAc
O OO
benzene80 ºC, 90%
OO
O
OOAc
H
H
H
0.1 CpRu+
0.15 CeCl3
DMF, 60 ºC80%
Mannich Reaction:
Interrupted three component reactionRu catalyzed coupling followed by Diels-Alder
Advantages of Multicomponent Reactions
• Complexity is generated through the combination of multiple functional groups.
• Diversity is easily incorporated in one step by varying the components.
• Deprotection steps are often avoided.• One pot reactions are ideal for automation.• Efficient solid phase or solution phase synthesis is
possible.
• Disadvantage: Generally cannot do split-pool synthesis
Two Component vs. Multicomponent Synthesis
• Three component synthesis can make 8 products in 4 fewer reactions than parallel two component synthesis.
A
A D F
A C F
A D E
A C E
A D
A CC
D
E
E
B D F
B C F
B D E
B C E
B D
B C
E
EB
C
D
F
F
F
F
12 reactions
A
A D F
A C F
A D E
A C EC, E
C, F
D, E
D, F
B D F
B C F
B D E
B C E
B
8 reactions
C, E
C, F
D, E
D, F
Three Component CouplingsParallel Two Component Couplings
• Split-pool two component synthesis can make 8 products in 4 fewer reactions than three component synthesis.
Multicomponent vs. Split and Pool Synthesis
4 reactions
AB D E
B C E
A D E
A C E
B C
A C
B D F
B C F
A D F
A C F
B D
A DB
C
D
pool
pool
E
F
pool
pool
Split-Pool Two Component Couplings
A
A D F
A C F
A D E
A C EC, E
C, F
D, E
D, F
B D F
B C F
B D E
B C E
B
8 reactions
C, E
C, F
D, E
D, F
Three Component Couplings
Multicomponent vs. Split and Pool Synthesis
• Parallel multicomponent synthesis:– Requires more steps– Does not require tagging– Often avoids deprotection steps– More easily automated
• Interrupted multicomponent reactions potentially could be used for split and pool synthesis.
The Multicomponent Ugi Reaction
O
R1 HH2N
O
OHR3 R4NC N
R1
O
NH
R2
O
R3 R4R2
A Domling and I. Ugi ACIEE 2000, 39, 3169.
• In the Ugi reaction, an aldehyde, an amine, a carboxylic acid, and an isocyanide couple to form an α-amino acylamide.
– Reactions usually are run in methanol or ethanol at high reagentconcentrations (0.5 to 2 M).
– Exothermic, ice bath cooling is often required.– Precondensation of the amine and aldehyde can improve yield.– Lewis acids can accelerate the reaction.
Preparation of Isocyanides
• Only 12-15 isocyanides are commercially available.• Isocyanides can be prepared by dehydration of a formamide or
derivatization of another isocyanide.
G. Skorna and I. Ugi ACIEE 1977, 16, 259. R. Obrecht, R. Herrmann, and I. Ugi Synthesis 1985, 400. P. Tempest, S. Brown, and R. Armstrong ACIEE 1996, 35, 640.
NH
H
O
R
NEt3, CH2Cl20 ºC to 25 ºC
75-98%
R = 1º, 2º, or 3º alkyl, benzyl, aryl, etc.
R N C
HN(iPr)2, CH2Cl20 ºC to 25 ºC
53-89%
POCl3
OR:
NCNC
LiR-X
NC
R
RX = MeI, BnBr, or CyBr
ClCO2CCl3
Isocyanide Chemistry
• The isocyanide reacts carbene-like by the α-addition of both a nucleophile and electrophile.
A Dömling and I. Ugi ACIEE 2000, 39, 3169.
R4 N CR4 N C
nucleophilic
electrophilic
R4 N CE
NuNu-, E+
Mechanism of the Ugi Reaction
• The coupling occurs by isocyanide trapping of a reversibly formed iminiumand carboxylate, followed by an acyl migration.
A Dömling and I. Ugi ACIEE 2000, 39, 3169.
O
HO R3R1N
R2O
O R3
H
N
R1
O
NH
R2
O
R3 R4HN
R1
O
NR4
R2
O
R3
R1NR2
O
R1HR2 NH2
HN
R1R2
NR4
O
O R3
R4 N C R4 N C
Ugi Reactions in TOS
• The Ugi reaction gives more than twice the yield of the dipeptidefragment than does linear peptide coupling.
• Analog synthesis is also simplified.
S. Bauer and R. Armstrong JACS 1999, 121, 6355.
MeOHhexanes 25 ºC
NH2
59%CNZHN CO2H
CO2Me
CHO
OBn
ZHN
CO2Me
O
NNH
O
OBn
H
O
NH
N
NH
O
HN
O
NH
O
OCO2H
CO2Hmotuporin
subnanomolar protein phosphatase inhibitor
Stereoselective Ugi Reaction
• ZnCl2 forms a rigid chelate with the imine to control the stereoselectivity of the Ugi reaction.
I. Ugi et al. ACIEE 1995, 34, 1104.
MeOH-75 ºC
OAcO
AcOOAc NAc
NH2
CO2H
OHC
CN
OAcO
AcOOAc HN
NZnCl2
O
OAcO
AcOOAc NHAc
NNH
OO
ZnCl2
85%>99% ds
Ugi Reaction in DOS
• Ugi Reactions are highly utilized for DOS:
– High generation of diversity• All four components can be varied.• Components are commercially available.• Reaction variations access diverse structures
– Compatible with large library size• The reaction is amenable to automated parallel
synthesis.• Reactions can be run in solution or on the solid
phase.
Solid Phase Ugi Reaction
• A library of 96 sialyl Lewis x mimetics was synthesized on the solid phase by a four component Ugi reaction.
R. Armstrong, et al. JOC 1996, 61, 8350.
O OHOH
HO
N
NH
O
CO2Me
O
CONH2
O OHOH
HO
OOO OR
NHAc
HO
O
OHO
HOO
HO2C
OHAcHN
HO
HOOH HO
sialyl Lewis x
O OHOH
HO
CHO
CN CO2Me
HO2C
H2N
O
NH
2.5 eq.5 eq.
1 eq.
1 eq.
1. CH2Cl2, THF, MeOH, 25 ºC
2. 20% TFA in CH2Cl2
50%, high purity
HO2C
CO2H
Fluorous Phase Ugi Reaction
• Fluorous tagged Ugi products can be isolated from excess reagents by fluorous phase extraction.
D. Curran, et al. JOC 1997, 62, 2917.
OH
O
(Rfh)3SiRfh = CH2CH2C10F21
1. CF3CH2OH90 ºC
NH2
O
H
NC
N
O
(Rfh)3Si
HN
O
2. extraction with FC-72
(fluorocarbon)3. wash with
benzene
TBAFTHF, 25 ºC
N
OHN
O84%
>95% purity
17 eq.
17 eq.
17 eq.
fluorous phase(contains product)
organic phase(contains reagents)
Ugi Variation: Bifunctional Reagents
• Linking two of the reaction components results in the formation of cyclic products.
C. Hanusch-Kompa and I. Ugi Tetrahedron Lett. 1998, 39, 2725.
N
O
HN
O
EtO2C
O
CO2HNH2
CO2EtCN
N
CO2
H
NH
O
O
NEtO2C
MeOH
25 ºC
85%
Ugi Variation: Cyclization Strategies
• Ugi products can be converted to a diverse range of structures using various cyclization strategies.
T. Keating and R. Armstrong JACS 1996, 118, 2574.
NC
R1 CO2H
R2 NH2
R3 CHO
O
R1 N
R2
R3HN
O
Ugi
O
R1 N
R2
R3
SR4
O
N
R2
R1 R3
R5 R4
O
O
HORO
RO
NR2
O
R1
NH
N
OR2
R3
O
R
RSHAcCl
Ugi Variation: Cyclization Strategies
• An Ugi, ring-closing metathesis sequence can be used to make β-turn mimetics.
A. Piscopio, J. Miller, and K. Koch Tetrahedron 1999, 55, 8189.
CH2Cl2, MeOH25 ºC
NH2
HN
NHBoc
OHO2C
CHOCN CO2tBu
NNH
O
CO2tBu
HN
O
NHBoc
O
NH
O
CO2H
HN
O
NH2.TFA
1. Cl2(PCy3)2Ru=CHPhDCE, 80 ºC
2. TFA, CH2Cl225 ºC55%
N
O
Passerini, Wittig
• The Passerini three component reaction is like an Ugi reaction but
without the amine.
A. Dömling, et al. Org. Lett. 2001, 3, 2875.
LiBr, NEt3THF
O
O
H
OHNC
OHN
O
O
OH
O
PO(OEt)2
HN
O
O
O
OH
tBuO2C
tBuO2C tBuO2C
81%
N
OH
tBuO2C
O
OH
HO2C
(Et2O)OP
HO2C
(Et2O)OP
OH
N
OtBuO2C O
(EtO)2OP
O
OH
Multicomponent Cycloadditions
• A dienophile traps the reversibly formed diene for a three component Diels Alder reaction.
M. Beller, et al. Org. Lett. 2001, 3, 2895.
NMP, 120 ºC
O
H
O
NH2NH
O
O
N HN OONH
O
O
NH
NH
O
OO
Ac2Ocat. p-TSA
[4+2]
VII. Chemical Diversity
Hypothesis Based Research
- Success depends on the quality of the hypothesis- Enormous successes have been achieved using this approach- As the complexity of the problem increases our ability to make the initial hypothesis and to use results to make new hypotheses diminishes
Problem: Find a molecule that can block protein trafficking. Only hydrophobicity, polarity and hydrogen bonding capacity have an influence on the molecule’s ability to block protein trafficking
1
x
2
x
3
6
7
Hydro
phob
icity
Polarity
Hydrogen bond capacitysolution
molecule chosen based on the initihypothesis
5
x
4
x
Diversity Based Research
- Diversity based research- Success depends mostly on the
diversity of the library that is screened for a solution
- Hypothesis based research- Success depends on the quality of
the hypothesis, which in turn depends on the information available about theproblem and the complexity of theproblem
- Many problems in chemistry and biology are multi-variable problems for which it is difficult to make an accurate (productive) initial hypothesis
- Introducing a hypothesis into diversity based search (e.g. privileged structure) can significantly reduce the dimensionality or size of the space that should be covered
Diversity is a measure of howwell the available space iscovered and is independent of the complexity of a problem
x
1
2
x
3
4
x
6
5
7
x
molecule chosenbased on the initialhypothesis
Polarity
Hydrogen bondcapacity
solution
HypothesisBased
x
1
23
4
6
5
7
10
9
8
1115
13
12
14
16
17
18Polarity
Hydrogen bondcapacity
DiversityBased
solution
Diversity
N
NO
HO
CN
N
NO
HO
N
NO
HO
S
ON
O
EtO
HOO
N
O
EtO
HO
ON
O
EtO
HO
diastereoisomers
enantiomers
Building block diversity
Stereochemical diversity
N
N
OBr
O OH
S
HN
N
N
OBr
O OH
S
O
N
NH
OBr
O OH
S
OTosMeMe
HN
OO
Functional group diversity
Molecular framework diversity
Diversification Strategies
• The number of diversity positions used contributes to the total number of compounds in the library more than the number of building blocks used to diversify each of them
A B
A
B
D
E
F
C
200 buildingblocks at each diversity position
40,000 compounds (2002)
6 buildingblocks at each diversity position
46,656 compounds (66)
Building Block Selection
• Tools for building block selection– Databases of commercially available compounds that allow
substructure search, e.g. find all primary alcohols – Computer programs that choose a subset of n compounds
from a set of commercially available ones, retaining the diversity of the original set
• Desirable properties of building blocks– Commercially available
• Building blocks should be introduced using reactions that require the presence of a common functional group
– Compatible with the synthesis plan • A building block must contain only functional groups that
are compatible with reactions that will be used after the building block is introduced
• Order in which diversity positions are elaborated can alleviate some of the constraints
Building Block Selection
• Diverse physical and chemical properties
– hydrophobicity and hydrophilicity
– Hydrogen bond donors and acceptors
– Acidic and basic groups
– Size
II
IOMe
INMe3
+
hydrophobic hydrophilic
NH
NH
NH
RRR
O
H R
OH
R R
O
OH
acceptor donor accepor and donor
acceptor and donor
R
O
OH R
NH2R
O
NH
R
acidic basic neutral
MeHO
HOHO HO
Building Block Selection
• Biasing elements
– metal binding elements
– reactive groups
• nucleophiles
• electrophiles
Ph3P PPh3
R1 R2
H2N NH2
R1 R2 HO
N
OH R1
R2
R3
N
NR
R NH2 R SH
O
R
O
R1
R
Functional Group Diversity
• Functional groups can be a source of diversity
N
O
O
Br
OOH
H
S
NO N
O
N
Br
OOH
H
S
O
HN
S
OMe
OO
N
O
N
Br
OOH
H
S
OMe
Functional group diversity elements:
R R
N
HN
SAr
R R
ON
RR
OR
O O
sulfonylhydrazone
oxime ketone
NH
NH
O
RRR
NR
R
R NH
O
R
urea amine amide
R1 H
O
R1
HN R2
O
R1
O
NHR3
O
O
R2
O
R1 OR4
R2
O R3
HN
R1
R2
N NH
O
R1
OR2O
R3
R4
N S
O R2
R1
R3
N
N
R3
R3
R1
R2
R2O
O R1
SAr
O
O
R1 O
O
R2
R1 H
O
R1OH
R1 R3
OH
R3
R1 OR2
R1 NH
O
R3
R1 O
O
R3
R1 OH
O
Diversity Potential of a Functional Group
• TOS - One functional group is not a priori superior to any other• DOS - Diversity potential of a functional group is a part of a
library design
All transformations are achieved in one step
Stereochemical Diversity
Stereochemistry can be used as a source of diversity
Stereochemical diversity elements:- stereogenic center- plane of chirality- axis of chirality- double bond
ON
O
EtO
HO
ON
O
EtO
HO
ON
O
EtO
HO
diastereoisomers
enantiomers
Why is Stereochemical Diversity Important?
Different stereoisomers can have dramatically different properties.
Examples from asymmetric catalysis and chemical biology:
HN
NH
NH
O
S
N
HO
tBu OMe
PhHN
NH
NH
O
S
N
HO
tBu OMe
Ph
H
N
CN
NF3C
O
HCN
1. catalyst2. TFAA
+
10% ee 95% ee
Thalidomide
S-thalidomide: teratogen,causes severe birth defects
R-thalidomide: safe anti-nausea agent
NN O
HO
O O H
NN O
HO
O O H
This compound was originallyadministered as a racemic mixture
Stereochemical Diversity: TOS vs. DOS
• Palytoxin has 64 stereogenic centers. 2n stereoisomers are
possible, where n is the number of stereogenic centers. For
palytoxin there are 1.85X1019 possible stereoisomers!
TOS: The goal is to synthesize one stereoisomer. Kishiaccomplished a synthesis of one stereoisomer of palytoxin:Kishi et al. J. Am. Chem. Soc. 1994, 116, 11205.
Stereochemical Diversity: TOS vs. DOS
• Palytoxin has 64 stereogenic centers. 2n stereoisomers are
possible, where n is the number of stereogenic centers. For
palytoxin there are 1.85X1019 possible stereoisomers!
DOS: The goal could be to synthesize all stereoisomers in one synthesis, but not as a mixture of stereoisomers. In split-pool synthesis, each bead must contain one stereoisomer.
Synthesis of L-Hexoses
• Challenge: Develop one synthesis route that provides access to
all stereoisomers of the hexoses
• This could be an example of DOS
CHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HO
CHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HO
L-allose L-altrose L-mannose L-glucose
L-gulose L-idose L-talose L-galactose
Common Starting Material
S.Masamune, K.B. Sharpless et al. Science 1983, 220, 949
Total Synthesis of L-Hexoses
• Sharpless epoxidation is used to establish the stereochemistry of
the two stereogenic centers
• The Payne rearrangement allows functionalization of the terminal
carbon atom
OOH
Ti (OiPr)4(+)-DIPT
t-BuOOHDCM92%
ROOH
O PhSH, NaOH
H2O - t-BuOHheat71%
ROOH
ORO
OH
OPaynerearrangement
RO
OHPhSH, NaOHH2O - t-BuOH
heat
OH
SPh
-SPh
R=CHPH2
Ph
Ph
S.Masamune, K.B. Sharpless et al. Science 1983, 220, 949
Total Synthesis of L-Hexoses
• The aldehyde was generated from the sulfoxide by a Pummerer
rearangement
MeO OMe
POCl3 (cat.)
RO
SPhOO
mCPBA
DCM, -78°C
RO
SOO
Ph
O-
+
NaOAc
Ac2Oheat
RO
SOO
Ph
O
+
Ac
H
-OAcRO
SOO
Ph+
-OAc RO
SOO
Ph
OAc
93%over 3 steps
Pummerer rearrangement
RO
OH
OH
SPh
Total Synthesis of L-Hexoses
• The stereochemistry at C-4 was diversified by establishing two pathways
for hemithioacetal hydrolysis, only one of which provides an opportunity
for epimerization to the thermodynamically favored configuration at C-4RO
SOO
Ph
OAc
RO
SOO
Ph
O-
RO
OO
O
H
RO
OO
O
H
thermodynamic product
K2CO3,MeOH, rt
DIBAL-HDCM, -78°C
RO
SOO
Ph
O-
RO
OO
O
H
no epimerization under the reaction
conditions
RO
OO
O-
H
Total Synthesis of L-Hexoses
RO
OO
O
H
RO
OO
OH
RO
OO
OH
RO
OO
OH
O O
RO
OO
OO
SPh
RO
OO
OO
SPh
RO
OO
O
H
RO
OO
OH
RO
OO
OH
RO
OO
OH
O O
RO
OO
OO
SPh
RO
OO
OO
SPh
1. Ph3PCHCHO(E:Z>20:1)2. NaBH, MeOH
SAE, (-) DIPT84%
SAE, (+) DIPT76%
1. Ph3PCHCHO(E:Z>20:1)2. NaBH, MeOH
SAE, (-) DIPT73%
SAE, (+) DIPT76%
1. NaOH, PhSHH2O - t-BuOH
2. 2,2 methoxy propane, POCl3
1. NaOH, PhSHH2O - t-BuOH
2. 2,2 methoxy propane, POCl3
1. NaOH, PhSHH2O - t-BuOH
2. 2,2 methoxy propane, POCl3
1. NaOH, PhSHH2O - t-BuOH
2. 2,2 methoxy propane, POCl3
Example of Reagent-Based Stereocontrol in DOS
RO
OO
OO
SPh
RO
OO
OO
SPh
RO
OO
OO
SPh
RO
OO
OO
SPh
CHO
HOOH
OHHO
HO
RO O
O
CHOO
O
RO O
O
CHOO
O
RO O
O
CHOO
O
RO O
O
CHOO
O
RO O
O
CHOO
O
RO O
O
CHOO
O
RO O
O
CHOO
O
RO O
O
CHOO
O
1. mCPBA2. AcOH, NaOAc3. DIBAL-H
CHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HOCHO
HOOH
OHHO
HO
1. TFA - H2O2. H2, Pd-C
1. mCPBA2. AcOH, NaOAc3. NaOMe, MeOH
A = B = C =
C C C C C C C C
B B B BA A A A
L-allose L-altrose L-mannose L-glucose L-gulose L-idose L-talose L-galactose
RO
OO
O
H
RO
OO
O
H
ROOH
N
NO
HO
CN
N
NO
HO
N
NO
HO
S
ON
O
EtO
HO
ON
O
EtO
HO
ON
O
EtO
HON
N
OBr
O OH
S
HN
N
N
OBr
O OH
S
O
N
N
OBr
O OH
S
O
Tos
Me
Me
HN
O
O
ON
O
EtO
HO
NH
OBr
O OH
N
HN
O
HO
S
Molecular frameworks
Molecular Framework Diversity
• Molecular framework (MF) is the largest structural element present in
all (or a subset of all) the members of the library
Why is Molecular Framework Diversity Important?
Different molecular frameworks impart different activities
OO
H
Me
OH
OO
OHHO
HO
OH BzO
paeoniflorinAnti-inflamatory activity
O
O
O N
O
O
Me
O
O
OMe
Me
H OH
Me
OMeMe
Me
OH
Me
OH
H
H
OMe
Me
rapamycinImmunosuppressant
NB
O
PhPh
Me
H
Me-CBS catalysCatalytic enantioselective ketone reduction
Molecular Framework Diversification Strategies
• MF transformations: convert a single MF to another one
– Trans-annular reactions - intra-framework bond making
• Trans-annular reactions in TOS
– Fragmentation reactions - intra-framework bond breaking
• Fragmentation reactions in TOS
– Fragmentation-trans-annular reaction sequences in TOS
– MF transformations in DOS
• Diverse MF synthesis: synthesis of a large number of MFs
– Linear vs. scaffold based library synthesis
– Substrate controlled MF synthesis-folding pathways
– Reagent controlled MF synthesis-branching pathways
Transannular Reactions in TOS
• Transannular Michael reaction
SPh
O
O
H
H0.1 eq PhSNa
THF, reflux, 12h93%
O-
O
H
H
SPh
H
H
O O
H
H
-O O
PhS H
H
PhS-
H. W. Moore Org. Lett. 1999, 1, 375
1 bond 3 stereocentersvicinal chiralquaternary centers
Fragmentation Reaction
• Molecular framework diversification
Nu
O
H
H
OR Nu
Et2AlCl, DCM
4h, 25ºCR5
O+
O
H
H
OR Nu
O
R5
O
H
H
OR Nu
O
R5
130ºC, neat
Ar atm.
RO
O
E. Winterfeldt et al., Chimia 1993, 47, 39
retro-DA
retro Diels-Alder fragmentation
Fragmentation Reactions in DOS
• Molecular framework diversity
O
H
H
O
O
H
H
OR Nu
O
R5
OR
O
Nu
R5
O
O
H
H
OR
NuR5
O
Δ
Nu
175 compounds
5250 compounds 5250 compounds
Examples of Diversity from Biosynthesis
Terpene Diversity
• Wide structural diversity and topological complexity in terpenoid molecules originate with isopentenyl pyrophosphate (IPP) and dimethallylpyrophosphate (DMAPP)
O
MeOH
AcO
HO
O
O
Ph
O
OH
Ph
PhCO2 OAcO
O
O
O
O
O
O
HO
t-Bu
HOHO
HO
OPP OPPDMAPPIPP
HN
CO2HHO
O
O
OH
Me
O
S-CoA
+
acetyl-coenzyme AGibberellic acid
Cholesterol
Taxol
Ginkolide B
proto-Daphniphylline
Biosynthesis of IPP and DMAPP I
• All terpenes derived from IPP and DMAPP
– Isopentenyl pyrophosphate (IPP) and dimethallyl pyrophosphate
(DMAPP) biosynthesized from acetyl coenzyme A
Me
O
S-CoAMe
O
S-CoA
NADPHO
O
OH
Me OH ATP
Me
O O
S-CoA
O
O
OPP
Me OPP
Me
O
S-CoA
[-OPP]
[-CO2]
O
O O
S-CoA
Me OH
IPP
Me
OPP
acetyl coenzyme Aacetyl-CoA thiolase
Claisen
HMG-CoAsynthetase
Aldol
HMG-CoAreductase
HMG-CoA
mevalonic acid
Biosynthesis of IPP and DMAPP II
• Stereospecific removal of the pro-R proton in IPP results in all-trans poly-
isoprenylated chains
H+
PPO
B
Me
Me
Me
OPPHR
IPP
HS
Me
OPPHR
BHS
Me
Me
OPP
DMAPP
Me
Me Me
OPP
PPO
Me
Meisomerase
prenyltransferase(s)
ionize
TERPENES
geranyl pyrophosphate
IPP
Diversity Via Multiple Cyclization Pathways
• Diverse and complex terpene structures are obtained via a wide range of cyclization/rearrangement pathways
– Terpene cyclase proteins mediate the cyclization process
O
M e M e
M e
O PP
O H
O
O
OO
O
G eranyl pyrophosphate
Taxol Biosynthesis
• Taxol skeleton produced by taxadiene synthase mediated cyclization of geranylgeranyl pyrophosphate (diterpene)– Initial folding /cyclization events leading to the formation of the
cationic macrocycle are enzyme mediated (reagent control). Subsequent intramolecular proton transfer is under substrate control
Me
Me
Me
Me
OPP
Me
H
MeMe
Me
Me
OH
OHO
AcO O
RO
OBz OAc
Taxadiene
synthase
oxidativemodification
TaxolThree stereocenters andthree rings from GGPP!
Williams, R.M., et al. Chem. Biol. 2000, 7, 969-976
Modular Polyketide Synthases
• To make chains of non-repeating units, modular PKSs have a
separate set of FAS-like domains (modules) dedicated to each chain
extension
KS
SO
Me
AT ACP
CoA-SO
Me
AT
CoA-S
O
OH
O
Me
KRACP
SH SO
Me
KS
SH
KS ATKR
ACP
SO
MeOH
Me
NADPH
SO
MeOH
Me
KS etc.
ATKR
ACP
SO
CO2HMe -CO2
KS
SH
ATKR
ACP
SO
MeO
Me
LOAD MODULE 1
1
Propionyl CoA
Methylmalonyl CoA
MODULE 1
2 3
MODULE 1
MODULE 1
4
MODULE 2
1) The AT of the load module loads the KS of module 1 with propionyl CoA
5
2) The ACP is loaded with methyl malonyl CoA by the AT of module 1
3) Decarboxylation and attack on the KS-bound propionate gives the extended β-ketothioester
4) The KR reduces the β-ketothioester
5) No more reductive modules are present, so the chain is transferred to module 2
Erythromycin Biosynthesis
• Three large modular PKS enzymes (DEBS 1-3), encoded by eryAI, eryAII,
and eryAIII, assemble the polyketide chain that forms the core of
erythromycin
O
O
Me
Me
Me
OH
Me
OH
O
Me
Me
OH
6-Deoxyerythronolide B
TE cyclizes
Staunton, J. Chem. Rev. 1997, 97, 2611.
• each module performs one chain extension
Pieper, R.; Kao, C.; Khosla, C.; Luo, G. Cane, D. E. Chem. Soc. Rev. 1996, 297. and refs therein
Erythromycin: DEBS Engineering - Deletions
• Normal:
• 80 aa deletion in the module 5 ketoreductase of DEBS
3:
• Mutation in the NADPH-binding site of the module 4
enoylreductase of DEBS 2:
O
O
Me
Me
Me
OH
Me
OH
O
Me
Me
OH
6-Deoxyerythronolide B
O
O
Me
Me
Me
OH
Me
O
O
Me
Me
OH
O
O
Me
Me
Me
OH
Me
OH
O
Me
Me
OH
Erythromycin: DEBS Engineering - TE Transposition
• Normal:
• Fusion of TE (from DEBS 3) onto DEBS 1:
• Fusion of TE (from DEBS 3) onto DEBS 2:
Pieper, R.; Kao, C.; Khosla, C.; Luo, G. Cane, D. E. Chem. Soc. Rev. 1996, 297. and refs therein
O
O
Me
Me
Me
OH
Me
OH
O
Me
Me
OH
6-Deoxyerythronolide B
O
OH
Me Me
O
O
Me
O
Me
Me Me
OH
Me
OHO
Erythromycin Biosynthesis
• A sequence of tailoring enzymes further functionalizes 6-DEB to give
erythromycin A
O
O
Me
Me
Me
OH
Me
OH
O
Me
Me
OH
O
O
Me
Me
Me
OH
Me
OH
O
Me
OH
Me
OH
OHO
NMe2
Me
OH
O
O
Me
Me
Me
O
Me
O
O
Me
OH
Me
OH
OHO
NMe2
Me
OMe
OH
OHMe
O
O
Me
Me
Me
O
Me
O
O
Me
OH
Me
OH
OHO
NMe2
Me
OMe
OMe
OHMe
HO
OH
OMe
OH
OHMe
Glycosyl-transferases
Selective hydroxylation
6-Deoxyerythronolide B
D-desosamine L-mycarose
+
Selective hydroxylation and
methylation
Erythromycin A
Staunton, J. Chem. Rev. 1997, 97, 2611.
Construction of Polypropionates - Nature, PKS
• 4 reagents• Complete reagent
(enzyme)-based control
HO
O
Me Me Me
OH OH OH O
Me Et Me
Me Me
MeO
Me Me Me
OH OH OH
O
Me
H
MeO2C
Me Me
OH
Me Me
Me
H
Me
OH
Me
OH
Me
OAc
Me
HO2C
Me
OMe
CHO
Premonensin
Me S-CoA
O
S-CoA
O
MeZincophorin
Rifamycin S(aliphatic fragment)
+
recombinant PKS enzymes
claisen condensations
reductions
A: Evans, D. A.; DiMare, M. J. Am. Chem. Soc. 1986, 108, 2476.B: Danishevsky, S. J.; Selnick, H. G.; DeNinno, M. P.; Zelle, R. E. J. Am. Chem. Soc. 1987, 109, 1572.C: Nagoaka, H.; Rutsch, W.; Schmid, G.; Iio, H.; Johnson, M. R.; Kishi, Y. J. Am. Chem. Soc. 1980, 102, 7962.
Construction of Polypropionates - Laboratory
• Many reactions
• Heavy reliance
on substrate-
based control
makes each
molecule a new
problem
HO
O
Me Me Me
OH OH OH O
Me Et Me
Me Me
MeO
Me Me Me
OH OH OH
O
Me
H
MeO2C
Me Me
OH
Me Me
Me
H
Premonensin
Me
OH
Me
OH
Me
OAc
Me
HO2C
Me
OMe
CHO
Zincophorin
Rifamycin S(aliphatic fragment)
Sigma-Aldrich Catalog
Ref. A
Ref. B
Ref. C
aldoldirectedreduction
alkylation
aldol
alkylation
grignard addition
hetero-D.A.
hetero-D.A.
hydroboration
Wittig;hydroboration
allylation
epoxidation
epoxideopeningWittig;
hydroboration
