1. Rapid Chemical Space Exploration – Applications from Discovery to Manufacturing Neal Sach Senior Principal Scientist Science Centre Drive La Jolla, CA 92121, USA ACS Technical Achievements in Organic Chemistry Philadelphia, USA August 22nd 2012
The Evolution of Reaction Optimization Technologies

2. Contents An Introduction to Reaction Optimization Workflows
Reaction Optimization in Process Chemistry
Adapting to Discovery Chemistry
Case Examples
First item is short as with the audience its preaching to the choir

3. Solving Chemistry Across the Portfolio
Discover Drugable Molecules
Supply Drug Substance
Develop Commercial Processes
Transfer Technology to Production
How we do this in less time and at a lower cost?
Supply Chain
Discovery
Process
Research
Development
Manufacturing
Covalent Bonds
Reaction Conditions
Work Up Conditions
Variations

4. Adapting to Industry Pressures
Technology must ‘fill the gap’
Workload
Resources
Apologies for showing this slide! Nice thing though is that its lasted two decades.
199X
20XX

5. The First Reaction Optimization Tool
In 1998 a Process Research Technology Group was created with the aim of speeding Process Development
The SK233 was the first tool of its kind, 10 simultaneous reactions with integrated analytics
1g per reaction, 10 reactions, 10-50ml volume
One instrument and an 18 year old just out of school! 3 reactions a day was considered acceptable, how could we improve that? 10 reactions per day was a start plus the integrated analytics provided a large amount of information per reaction. This was a significant improvement on current productivities.
Primary amide could be followed and we could see how long the reaction actually was, compared with just leaving it overnight.

6. UK-427,387 – The Tipping Point
Despite a few successes, the general adoption of the SK233 and reaction optimization technologies was slow…
…but that was to change…
UK-427,387 was nominated as a follow up PDE5 inhibitor to Sildenafil (Viagra)
Culture paradigm shift.
Material requirements (10g per run!).
Technical failures.

7. UK-427,387 Pyrazole Alkylation
25kg Required for Phase 1
Issues (where to start?!)
30% overall yield
2:1 undesired : desired pyrazole
7 days reaction time, complex conditions (4 solids, 2 solvents)
5-14% undesired alkylated isolated
Parallel Synthesis Robot (PSR)
250mg per reaction, 50 reactions, 5-25ml volume
Selectivity the wrong way!
Project team had 6-week deadline.
Almost forced their hand to work with the technology

8. UK-427,387 Pyrazole Alkylation
New Conditions
Results
30:1 selectivity achieved
12hrs vs. 6 days reaction time
Scaled to 32kg, 71% isolated yield of 99% purity
25kg Required for Phase 1
Screen
120 reactions run over 3 weeks
12 bases x 10 solvents
Strong base required
Lithium count-ion needed
MeCN solvent found to be key
Before
After
1:2 N1:N2
30:1 N1:N2
120 reactions in 3 weeks doesn’t seem like much now.
Note the HPLC run-time! 10 minutes!
This chemistry was a game changed and people begun to see the potential for reaction screening technology
Q. Would this obscure hit have been found in the short time frame allowed without reaction screening technology?

9. Development of High Throughput Experimentation (HTE) Workflows 2002-2005
Solids
Dispensing
Rational
Design
Statistical
Methods
Reaction
Execution
and Analysis
Data
Capture and
Visualisation
Data
Analysis
Reaction
Platform
Reaction
Platform
Fast
Conclusions
Chemists
Liquids
Dispensing
Data
Mining
Over the next 3 years there was a significant investment in new technology, increased resource and the HTE workflow evolved over time.
Emphasis on fast conclusions that can be used to make decisions. Particularly useful for alternative routes.
5Higginson, Paul D.; Sach, Neal W. High-Throughput Experimentation in Pharmaceutical Process R&D: Developing a New Software Workflow to Overcome
Downstream Data-Analysis Bottlenecks and Improve Productivity. Organic Process Research & Development (2004), (8),

10. 2002-2005 Investment in Technology
By 2005 the HTE group in Process had expanded to 5 FTE’s with state of the art equipment at their disposal
25mg per reaction, 50 reactions, 1-2ml volume
2ml
Reaction
Volume
One 2 Many Weighing
iChemExplorer Reaction Platform
2-4 minute HPLC cycle-time per sample
Explain past experience with all in one systems Detail each piece of technology
Explain miniaturization
Analytics are key to high-throughput
Fast HPLC
Analysis Platform
High-throughput analytics and generic methods are critical to HTE Modular Workflows
Gaseous Chemistry
Many 2 Many Weighing

11. Application of High Throughput Chemistry Workflows Across the Portfolio
Discovery
Process Development
Supply Chain
Applications
Solubility Profiling
Solid Form Identification
Reaction Screening
Start
Resolution Screening
Explain four categories
Reaction Screening
Chiral Methods – Resolution Screening, Biotransformation Screening, Asymmetric Hydrogenations
Salt Screening – Solid form of intermediates generally to ease isolation
Solubility Screening - Understanding of solubility to ease work-up
Also that the technology was applicable across the portfolio, both in discovery and, development and even in supply chain and from flow to batch screening. In this talk we are going to focus on reaction optimization and expanding chemical space in Discovery as

12. Example Workflow - Resolution Screening
Scalable access to chiral molecules via diastereoisomeric salt formation
Resolution Coupling Protocol :
96 Chiral Acids or Bases
1 Solvent
10-20mg per reaction : 2g Total
0.5 FTE Days
1 Day Start to Finish per Solvent
Explain resolution process

13. Example Results of Resolution Screens
Generally Chiral SFC is always the first port of call for Discovery chemists.
However this is now changing especially as molecules move towards FIH.
Resolution screening is successful in 80% of cases
Zhou, Ru; Bi, Chris; He, Mingying; Hoffman, Robert; Jalaie, Mehran; Kath, John; Kupchinsky, Stan; Ling, Tony; Lu, Jihong; Marx, Matthew; Richardson, Paul; Sach, Neal; Tran, Khanh; Barbour, Nicole; Cho-Schultz, Su.
Asymmetric synthesis of Pyrrolodino-pyridine based CXCR4. Abstracts of Papers, 240th ACS National Meeting, Boston, MA, United States, August 22-26, (2010)

14. Example Workflow - Solubility Screening
Isolating good quality material can be as difficult as forming the covalent bonds
Problematic isolations may result in large quantities of organic and aqueous waste streams and loss of product
Traditional Reaction Sequence
Bottom-up approach to Reaction Design
Driven by solubility screening
Reaction
Solvent
Low Solubility
of Product
High Solubility
of Bi-products 1.
Design Reaction 2.
Run Reaction 3.
Analyse Reaction 4.
Design Work-up 5.
Work-up Reaction 1.
Design Reaction 2.
Run Reaction 3.
Analyse Reaction 4.
Design Work-up 5.
Work-up Reaction

15. Example Results of Solubility Screens
Objective:
Map solubility of all synthetic intermediates in range of process solvents
HTE Workflow:
20 solvents screened as standard chosen by chemist
Solution saturated and liquors analysed
Quantitative LC
Typically applied to entire synthesis
250mg-1g per screen in 0.5 Day
Data enables logical decision on reaction solvent when given choice.
This is often the case from HTE experimentation results.

16. 2007 - Bringing HTE to Discovery
1 FTE!!
…the workflow was not designed for this throughput and was too slow…
Process Projects
5 FTE’s LJ
Sandwich
Explain Reaction Optimization workflow and its evolution over time.
M wife was not happy that year.

17. Reaction Optimization in Process
Experimental Set-Up
Project Team Problem x2 x1
X n
Experiment Design
Reaction Analysis
Answer
Workflow no different to normal chemistry problem but automation enables numbering.
Results Interpretation
Cycle 2 = 4 days
Cycle 3 = 6 days
Cycle 1 = 2 days

18. 2007 - The Discovery Experience
Discovery chemists want answers…
…faster and using less material compared with process development
…and they have no product markers!
ESD – Exploratory
Screen Development
SDS – Screening
/ Designed
Synthesis
LD – Lead
Development
CS – Candidate
Seeking
Early
Development
Discovery
Speed █
Diversity █
Yield █
Isolation █
Scalable █
Process Development
Scalable █
Yield █
Isolation █
Speed █
Diversity █

19. Speeding the Workflow
Challenge over the past three years has been to speed the workflow by removing the bottle necks
Where is the time spent?
These steps needed addressing
Reaction
Design
Reaction
Execution
Semi-
Automated
and fast
20%
Analysis
and
Visualisation
Semi-
automated
and slow
30%
Manual
and slow
50%
Scouring the literature and designing a custom set of reactions is rewarding but very time consuming. Digging through the literature much of which is poor quality

20. Designing a Reaction Screen in Process
Intelligent Reaction
Design
Chemists
and
CeN
Statistical
Methods
Green
Chemistry
Principals
Literature
Surveillance
Literature surveillance involves a group monitoring transformation and creating a network of surveillance so that new literature does not fall through the net

21. Screening Chemical Space
…searching the literature on a per screen basis helps us move into the “correct” chemical space but if the chemistry doesn’t work in this initial screen we spend a lot of time searching or settling at local maxima…
…what if we moved to a more generic one-size fits all type template… that would save time but…the chemical space covered increases dramatically…
…besides...was we ever really comfortable excluding this space?
will you ever find something new?
Large Reaction Template
Unchartered
territory
Cycle 2 = 4 days
Cycle 3 = 6 days
Cycle 1 = 2 days
Base
Literature Says
Start Here
Solvent
Catalyst

22. Literature Misdirection
Sonogashira Reaction
Project team report poor yields using standard conditions
Literature Search
161/161 references utilize Pd(Ph)4)3 or Pd(P(Ph)3)Cl2
What have we really learnt?
Precedent (we knew that)
%Area UV
50%
50˚C ˚C
Apologies for the R group. Explain spotfire plot, first instance.
This catalyst combination is unprecedented for Sonogashira reactions but likely because it was quite recently invented.
Explain Spotfire
161 literature
conditions
Mass Ion
Count
Un-precendented

23. Increasing Chemical Screening Space vs. Material Demands
…discovery project teams cant afford >500mg of material for each screen, in-fact they would like to reduce the amount required…
WE NEED TO MINATURIZE (but without diluting)
20 Reactions=100mg 200 Reactions=100mg
1.2ml
Reaction
Volume
120uL
Reaction
Volume
2007 to
2011
This magnitude reduction has resulted in less material being required and a much larger reaction space being examined

24. Reducing Scale – Air/Moisture Sensitivity
With just 0.04mg of catalyst present the workflow had to be moved into a glove box with a controlled O2 (<10ppm) and H2O atmosphere (<20ppm)
Scale (400MW)
7.5mg, 0.02mmol
0.75mg, 0.002mmol
Catalyst (400MW, 10mol%)
0.4mg, 0.002mmol
0.04mg, mmol
12x32mm
1.2ml
8x30mm
120uL
This magnitude reduction has resulted in less material being required and a much larger reaction space being examined

25. Projects by Reaction Type
Templated :
Suzuki Couplings
Buchwald Couplings
Amide Couplings
Heck Couplings
Carbonylations
Classical Resol.
Alkylations
Hydrogenation
Sonogashira
Ullman Couplings
Halogenations
etc...

26. Speeding the Workflow
For templated chemistry (60%) the workflow is significantly faster….
…but analytical samples have increased by a magnitude…
Reaction
Design
Reaction
Execution
Semi-
Automated
and fast
30%
Analysis and
Visualisation
Semi-
Automated
but slow
60%
Templated
Chemistry
10%
Reaction design consists of check the literature that the expanded screen covers the reported conditions (almost always does)

27. Data Analysis, Capture and Visualisation
Capturing data, identifying products, analysing trends and reaching quick conclusions
iChemExplorer Data Capture
Rapid Resolution 1200 LC/MSD
Per sample cycle-time
dropped from 4 to 0.8mins
data points per reaction screen. 100 reactions take 1.5hrs
report and then capture in CeN as well as in-house reaction screening database
Mention the lack of marker in Discovery
Spotfire Visualization with Data Display
Data to knowledge in 1 hour
6Mathews, B. T.; Higginson, P. D.; Lyons, R.; Mitchell, J. C.; Sach, N. W.; Snowden, M. J.; Taylor, M. R.; Wright, A. G. Improving quantitative measurements for the evaporative light scattering detector.
Chromatographia (2004), 60(11/12),

28. Discovery Orientated Screening Workflow
…combining reaction templates with miniaturization and glove box technologies has enabled a reduction in material demands and reduced screen cycle times leading to an increased applicability to Discovery Chemistry
Days per Screen
Explain Reaction Optimization workflow and its evolution over time
A templated reaction screen of >100 conditions is now turned around in 24hrs

29. Examples Amide Bond Formations Carboamidation Technology C-N Couplings
Explain Reaction Optimization workflow and its evolution over time

30. Amide Bond Formation – A Discovery Problem
25% of all reactions in discovery involve amide couplings
Large numbers of coupling agents are commercially available
Which one?

31. Difficult Amide Bond Formations - Discovery
70%
1. T3P
2. 1Cl2MPyI
60%
1. Cyanuric Fluoride
2. 2C-DMI-TFB
Sterically
hindered
Selectivity
Amide Coupling Protocol :
36 Coupling Agents
2 Solvents, 2 Temperatures, 1 Additive
150 reactions = 90mg total (300MW)
0.5 FTE Days
2 Days Start to Finish
50%
1. (COCl)2
2. CDMT
3. iBuCOCl
4. HATU
60%
1. TPTU
2. TDBTU
3. TOTT
Point to note here is that different coupling agents offer advantages and that HATU is not always the best answer.
Fix’s identified in Discovery are inherited by process.
Resource spent must be low though.
This also enables more accurate complexity scoring and allocation of resources.
Electron
poor
amine
Selectivity

32. The Amide Bond – Expanding Monomer Space
The amide bond remains a popular connection in drug discovery to explorer SAR….
…but there are other way of making an amide bond and a monomer analysis reveals the advantages…
ArCOOH
6441
ArCl, Br, I, OTf
14136
Traditional Coupling
Overlap 725 (3.5%)
Carboamidation Coupling

33. Carboamidation – Accessing New Chemical Space
Carbonylation Screen
Details
Method required for primary, secondary and non-nucleophilic amines
78 Conditions (0.005mmol, 1mg per reaction)
12 catalyst/ligand (combinations (all monomers)
56 catalyst/ligand combinations (one monomer)
DMAc (0.03M), DIPEA (5eq.), 100C, 8Bar CO
Technology

34. Carbonylation Library Validation
Conclusions
Ligand system works across all demonstration monomers
Library 1 = 88 designed products
82 / 88 achieved = 93% success 0.05mmol scale. How would acid compare?
500 products have since been prepared using these conditions (2 weeks)
Carbonylation Screen
Details
Take top eight ligands from initial screen and run under actual library conditions
78 Conditions (0.05mmol=10mg per reaction)
8 catalyst/ligand combinations
3 monomers (3eq.)
DMAc (0.1M), DIPEA (5eq.), 100C, 4Bar CO
Comments
SM is not soluble at this concentration at 25C. Solids weighing robot is used to weigh 80 x 10mg
$73/g
$640/g

36. Suzuki Optimization %Area UV 80% Issue Screen Design Results Mass Ion
MeOH / CsF(aq.) /
Pd-132 // 80C / 18hrs
Issue
Team tried DME / H2O / Pd(dppf)2Cl2 / 80°C but gave only 50% conversion after 2 days
Screen Design
96 conditions (0.003mmol, 1.13mg)
110mg for screen
6 catalyst/ligand combinations
4 bases and 4 solvents
80C, 18hrs, glove box
Results
1/96 conditions gave >80% in-situ yield
MeOH, CsF and Pd-132 are critical. Three factor interactions are hard to find. One factor at a time optimizations wont work here.
Request to Results Cycle Time = 1day
Scaled to 200mg, 90% isolated yield
Request to Registration Time = 2days
Original
Conditions
Mass Ion
Count
Product
Des Bromo

37. Conclusions KNOWLEDGE PER GRAM PER UNIT TIME
Maximize information per reaction
Minimize material consumption
Minimize time to explore any given chemical space
Using HTE Workflows, optima within a given parameter space can be quickly identified to focus resource at any stage across the portfolio
1g/rxn
X 10
100mg/rxn
X 50
10mg/rxn
X 100
1mg/rxn
X 200
0.05mg/rxn.
X 1000
1998
2001
2004
2007
2012

38. Acknowledgements Technology Chemistry Special Thanks Carol Baines
David Bernhardson
Klaus Dress
David Damon
Bill Farell
Stuart Field
Steve Fussell
Rob Maguire
Ben Matthews
Andrew Morrell
Paul Richardson
Steve Trudel
Alex Wilder
Katie Wilford
Alex Yanovsky
Chemistry
Kevin Bunker
Laurence Harris
Bob Hoffman
Peter Huang
Sarah Lewandowski
Sacha Ninkovic
Dan Richter
Hong Shen
John Tatlock
Special Thanks
Simon Bailey
Rob Crook
Peter Dunn
Klaus Dress
Martin Edwards
Paul Higginson
Jennifer Lafontaine
Ivan Marziano
Steve Trudel
Paul Richardson
Pete Spargo
David Waite
Mike Williams
Alex Yanovsky