1. Building Blocks for Big Pharma
Contract Research Experience 2001-2005
This presentation is dedicated to Theodora Greene. Her book “Protective
Groups in Organic Synthesis” provided me with the idea to use thiols to
liberate pyrrole-3-carboxylic acids; an idea that resulted in a step forward
in my career.
2. Building Blocks for Pharma
Synopsis
• Executed and supervised the production of 250 high-quality,
unique building blocks and scaffolds for Big Pharma clients
• Responsible for planning and logistics to meet monthly quota
(= # of compounds x complexity)
• Feasibility studies on proposed building blocks and direct
reporting to clients
• Responsible for quality of deliverables and accompanying
documentation
• Supervised team of Ph.D. and M.S. chemists
3. Pyrrole-3-carboxylic Acids, 2002
Pyrrole-3-carboxylates are prepared in high yield by a Michael addition of
an enaminoester with a nitroolefin, followed by intra-molecular acid-catalyzed
condensation:
Saponification should provide the building block…….
4. Pyrrole-3-carboxylic Acids
Synthetic scheme, increase diversity along the way
Feasibility study showed
R1: (substituted)-alkyl
R2: alkyl, benzyl
R3: alkyl, aryl, heteroaryl
R3 is the most effective source of diversity
5. Pyrrole-3-Carboxylic Acids
Diversity and Logistics
•Three points of diversity: alkylating agent (R1), amine (R2), and aldehyde
(R3)
•Find balance between diversity (client) and monthly quota (contract, cash
flow)
•Pyramid approach; introduce diversity late:
•Use commercially available diversity points
•Maximize throughput by scale-up of a limited # of labor-intensive
ketoesters
•Randomize diversity points to maximize use of (synthesized) stock
•Keep Mw< 300
6. Pyrrole-3-Carboxylic Acids
Diversity and Logistics
But most importantly:
•Develop a general procedure for expediency, accept lower
yields of outliers
•Avoid chromatography (loss of time, CRO responsible for
cost of materials)
7. Pyrrole-3-carboxylic Acids
Custom Ketoester/Enaminoester Synthesis
Generate ketoester dianion with NaH and n-BuLi; quench with
alkylating agent. 100-300 g Batches prepared; purification by vacuum distillation.
Leaving group X determines outcome!
8. Pyrrole-3-carboxylic Acids
Ketoester/Enaminoester Synthesis
A standard protocol for the synthesis of enaminoesters was developed by simply mixing
and rfx in THF/HOAc; the crude was carried forward:
Some representative examples:
9. Pyrrole-3-carboxylic Acids
Henry reaction/Knoevenagel; synthesis of nitro olefins
Purified by distillation (R3 = alkyl) or crystallization (R3 = aryl)
Selected examples
(Commercial)
10. Pyrrole-3-carboxylic Acids
Production strategy
Most building blocks designed around cheap, commercial ketoesters
Ketoester scale-up
One chemist
Scale-up nitroolefins
Team
} Commercial amine Complete building block
Individual chemist
Future use
11. Pyrrole-3-carboxylic Acids
Deprotection methylesters
Esters resist deprotection by saponification or with hard nucleophiles
Acid-catalyzed hydrolysis leads to unstoppable decarboxylation to “useless” pyrroles
12. Pyrrole-3-carboxylic Acids
Not quite an aromatic system…..
A pyrrole-3-carboxylate behaves as a vinylogous carbamate; resists
nucleophiles such as hydroxyl ion
Basic conditions:
A pyrrole-3-carboxylic acid, once formed, behaves as an
enamine, is protonated, and immediately decarboxylates
Acidic conditions:
13. Pyrrole-3-carboxylic Acids
Sulfur nucleophiles to the rescue
Keinan et al. described the alkoxydecarboxylation of ketoesters
and malonates by treatment with thiols and cesium carbonate
in hot DMF.
Thiophenols are most effective: JOC 51, 1986, 3165
14. Pyrrole-3-carboxylic Acids
Sulfur nucleophiles to the rescue
•Pyrrole-3-carboxylate is a soft leaving group, responds
to soft nucleophiles
•Initial success with thiophenol, but what about the stench?
•How to effectively remove excess thiophenol, a weak acid,
•From the acidic product?
15. Pyrrole-3-carboxylic acids
Use 4-Aminothiophenol for demethylation
•Commercially available (TCI Japan)
•$40 for 25 g (2002)
•No stench (faint licorice-like smell)
•Non-volatile
•Low-melting solid (a disadvantage)
•Better nucleophile that thiophenol
•Basic aminogroup would allow removal
by acid wash
16. Pyrrole-3-carboxylic acids
Loss of CO2 needs to be controlled
Loss of CO2 during deprotection with a sulfur nucleophile
is promoted by:
•Higher rxn temperature: > 110 oC
•Extended reaction times: > 12 h
•Higher concentration: > 0. 25 M
•Low pH: < 2 @ drop of product from extraction water
Standard conditions during production:
•2 eq. 4-aminothiophenol
•5 eq. K2CO3
•0.15 M in DMF at 100-105 oC
•Monitor with LCMS/ELSD, use in-process judgment
•Drop or extract product from aqueous at pH = 3-4
17. Graphic Presentation Optimal Conditions
- CO2 - CO2
0.25 M
Time
conc
0.1M
Low conversion Waste
No reaction Temp
- CO2
90oC pH 110oC
2
- CO2
18. Pyrrole-3-carboxylic acids
Results from production
•70+ Pyrrole-3-carboxylic acids of 95%+ purity* were
delivered in 8 months (3 FTE’s)
•Deliverables in 5-50+ g amounts
•Observations:
•Increase of steric hindrance (R1 or R3) leads to faster decarboxylation. In one
case upon storage at ambient
•“Greasy” substituents allow extraction of pyrrole-3-carboxylic acids from
basic aqueous layer. Acid purified by silica plug
* Purity per LCMS/ESLD x NMR purity (for residual solvents)
19. Pyrazoles and Isoxazoles, 2003
•The continuation of the collaboration depended on solid proposals
for the rapid synthesis of 30-60 building blocks in 5-50 g amounts
•Building blocks, acids or amines, needed to possess “medical chemistry”
characteristics: ideally low molecular weight heterocycles
•The synthesis needed to demonstrate versatility: introduce
maximum diversity by a general procedure to secure expediency
•Proposed to bank on experience with enaminoesters, starting materials
for pyrazole-3-carboxylic acids and isoxazole-3-carboxylic acids
•Design accepted by Client for production
20. Azole Template Series; A Need for Consistency
and Diversity
•Multiple chemists w/ minimal supervision
•Flexible staffing (easy procedures), influx
Moscow colleagues
•Few early intermediates
•Diverse, commercial building blocks
•Minimize outliers
Diversity
21. Azole Synthesis
Mechanistic Intermezzo
For isoxazoles, the more nucleophilic N-atom of H2NOH attacks
22. Pyrazoles and Isoxazoles
Enaminoesters; acylation
Near quantitative yields over two steps; no need for purification.
Selected examples for commercial acid chlorides:
23. Pyrazoles and Isoxazoles
Pyrazoles were designed by combining:
•R2 = aryl with hydrazine (R3 = H) or methyl hydrazine (R3 = Me)
•R2 = alkyl with substituted hydrazines, R3 = alkyl or aryl
Simple rfx of acylated enaminoester with hydrazine or hydroxylamine in THF
w/ HOAccat provided a high-yielding standard protocol. Two examples:
HCl avoids catalyst poisoning
Specific example proposed by Client
24. Pyrazoles and Isoxazoles
Alternate route, more diversity
An alternative entry to enaminoesters
Access to 5-substituted pyrazole and
isoxazole-4-carboxylic acids
For example:
Steric hindrance and lower nucleophilicity require harsher conditions for ring closure
26. Trifluoromethyl-substituted Pyrazoles
Developed by ongoing R&D during production to counter production attrition
and secure # of deliverables
Enaminoesters are cleanly acylated by TFA-anhydride providing access
to 3-trifluoromethylated pyrazoles:
Cu-catalysis provided an unprecedented (2002) regioselective N-arylation which was
confirmed with 2D-NMR
28. Pyrazole and Isoxazole-3-carboxylic Acids
Deliverables
•Delivered 51 building blocks, 20-25 g, >95% purity* in
8 months w/ 2.5 FTE’s
•Slower production pace, but much higher diversity than
pyrrole-3-carboxylic acid production:
additional chemistries per building block
more custom ketoesters
re-synthesis of fluorine-substituted building blocks
to meet post-delivery by Client
* Purity per LCMS/ESLD x NMR purity (for residual solvents)
29. Palladium Catalyzed Amination (2004)
Old Compound, Modern Approach
100 g negotiated as add. delivery
Denatured ethanol with 3% methanol gave methoxy-substituted quinolines
as major product
30. Old chemistry from 1982 notebook
Reflux w/, and distillation of large excess of piperazine
resulted in condenser and distillation head clogged
with sublimate.
Residual piperazine complicated purification.
31. Palladium Catalysis
New elegant chemistry
Ligand for less active C-Cl bond
Tri-hydrochloride, dihydrate
80% over two steps
A high-yielding palladium-catalyzed amination provides
solution to a practical scale-up problem.
32. Dihalopyridines in Negishi Chemistry
Client’s Proposal (2005):
Dibromopyridine:
•Difficult to make
•Instable
•Poor regioselectivity in palladium catalysis
Even after separation, assignment of regio isomers is not trivial;
a regioselective coupling would avoid this problem.
33. Alternative Halopyridines for Negishi Reaction;
Known, Stable, and Easily Accessible
A literature example hints towards regioselective Negishi
coupling at the 2-position of 2,4-dichloropyridine
34. Negishi
NMR fingerprint different from B;
Differentation by NMR confident assignment of 2-substituted
regioisomer
Assignment based on higher
reactivity of C-I bond
Careful choice of nucleophiles allowed delivery of two
pure and characterized building blocks.
35. Acknowledgement
I want to express my gratitude to my
colleagues at CRL that made it a great
place to work and achieve.
In particular I want to thank Gene and
Gala Vaisberg for showing that the deep
American plunge pays off if you work
hard.
