Parallel%20Synthesis%20A%20Useful%20Tool%20for%20Medicinal%20Chemistry

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Parallel SynthesisA Useful Tool forMedicinal
Chemistry
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Parallel Synthesis

• What is it? - A way to make molecules faster
• Why do it? - More efficient, less
  drudge/compound
• When do you use it? Lead generation, Lead
  optimization, Process development - Chemistry
  Driven
• How do you do it? We have some suggestions
• Who does it? Any Chemists who know Organic
  Synthesis

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Why?

• By using Biotechnology, Genomics, Computers,
  Robotics and Chemistry
• Biology got a lot faster.
• Adequately exploiting the biology requires
  greater synthetic throughput.

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4 Ways to go Faster

• Use Combinations
• Reuse (usually (A x B) gt (A B)/2) or
• multiplying gives bigger numbers than adding
• Do many things at the same time
• Parallel processing
• Speed up the process
• Microwave
• Get someone else to do it
• Automation
• Outsourcing

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Two Major Approaches

• Split Mix
• Real Combinatorial Chemistry
• Array Synthesis
• Parallel Synthesis

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Split Mix

• Real Combinatorial Chemistry
• Large diversity requires but can also utilize a
  longer synthetic sequence
• Generally makes a smaller amount (pM to nM) of a
  greater number of compounds
• Efficiency requires multiple sites (3 or more) of
  diversity
• Data handling, tagging schemes and analysis can
  be complex
• Generally applicable to only solid phase
  synthetic approaches

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Array Synthesis

• Parallel Synthesis
• Large diversity requires but can also utilize the
  large diversity of commercially available
  reagents
• More efficient when an array of reactions is
  treated as a unit parallel processing
• More efficient with 2 sites of diversity
• Data handling simpler - one site, one compound
• Applicable to both solid and solution phase
  synthetic approaches
• With micro-titer plate format, one can borrow
  equipment from biologists (a first)
• Efficiencies gained in matrix format make this a
  combinatorial technique
• Make greater quantities (uM to mM) of fewer
  compounds

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Solution andSolid Phase Chemistry

• Solution Phase Organic Chemistry is chemistry
  like it used to be (pre 1990).
• Solid Phase Organic Chemistry (SPOC) is chemistry
  where some part of the target molecule is
  covalently attached to an insoluble support
  somewhere during the synthetic sequence.
• Solid Phase Reagents (SPR) are insoluble reagents
  used in solution phase chemistry (like 10 Pd/C
  or polyvinyl pyridine). They (SPRs) may be made
  using SPOC. They (SPRs) have also made solution
  phase combinatorial chemistry easier.

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Solid Phase Organic Chemistry

• Products are insoluble
• Easier to manipulate physically
• Easier to clean up, can wash exhaustively
• Can use excess reagents to drive reactions to
  completion
• No bimolecular reactions (infinite dilution)
• Cant use Solid Phase Reagents (SPR)
• Modified kinetics (generally slower, greater rate
  distribution, all sites not equal)
• Requires laborious analytical methods
• Requires linking chemistry (limits reaction
  conditions, constrains product structure, adds
  steps)

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Solution Phase Organic Chemistry

• Products are soluble
• Byproducts and excess reagents are also soluble
  and accumulated with each step
• Direct analysis is much easier (tlc, nmr, ms,
  hplc, lc/ms)
• Kinetics are uniform and familiar
• Use of solid phase reagents (SPRs) is possible
• No linkers required, less excluded chemistry
• Requires development of parallel workup and
  purification methods

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Trends over the Last Decade
Sld P SplitMix
Sld P Array
10,000
Solution P Array 2004
of Compounds
1000
Solution P Array 1996
Classical Organic Synthesis
0
time
InnovaSyn targets Solution Phase Array synthesis
Dev. times for solid phase
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Guiding Principlefor Parallel Synthesis

• Keep it Simple Adding complex things to already
  complex environments doesn't work
• Make it look familiar easy to learn
• Limit the number of formats or footprints
• Use standard formats and footprints
• If it's faster, easier, and more flexible, do it
  manually
• Use one-to-one mappings rather than complex
  tracking to keep up with things
• Keep it in solution as much as possible
• Run reactions at equi-molar scale
• Find someone who has figured out much of this and
  work with them

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The ParallelSynthesis Process

1. Choose Chemistry
2. Prepare solutions Solution Station
3. Run reactions SynthArray-24 reactor and more
4. Analysis Automation with Transfer75/1
5. Workup Automation with Transfer75/1
6. Purifications Automation with Transfer75/1

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Choose Chemistry

• Actually, the chemistry is more likely to dictate
  whether parallel synthesis is applicable.

Multi-component reactions 2 step reactions with
multiple inputs Sequential parallel reactions
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SolutionPreparation

• Solution Station
• Enter Solvent, Target Volume, Concentration and
  Molecular Weight
• Weigh out Sample (roughly)
• Dispense Solvent
• Enter next weight

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SynthArrayReactors

• Solution Phase Chemistry Reactors
• Microtitier Format
• Various Sizes Disposable Glassware
• Reactor Vessels held at Top
• Add functionality (complexity) as needed

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SynthArray-24Reactors
Solution Phase Chemistry Reactor
Top with 24 holes Teflon-faced Silicone
Gasket Nitrogen inlet/outlet Tube holder
w/O-rings Condenser 24 Glass Reactor
Tubes Heater Block/Plate Alignment
Guide Thermocouple
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SynthArray-24Reactors
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1
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Parts
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SynthArray-24Reactors
Inserting tubes
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SynthArray-24Reactors
Removing Sleeve
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SynthArray-24Reactors
Simple Reaction
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SynthArray-24Reactors
Inert atmosphere setup
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SynthArray-24Reactors
Low temperature reaction under inert atmosphere
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SynthArray-24Reactors
Reflux reaction under inert atmosphere
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SynthArray-24Reactors
Reaction under reactive atmosphere
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SynthArray-24Reactors
Recirculating temperature control
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SynthArray-24Reactors
Stir bar removal
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Commercial Reactors
Best Choice
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SynthArrayReactor Summary

• Simple Design works like a round bottom flask
• Compact design - easily fits in a drawer when not
  in use
• Multiple Scales 1 to 60 mL
• Inexpensive sealable disposable glass vials
• SynthArray-24 8 mL screw cap culture tubes
• SynthArray-6 20, 40 or 60 mL screw cap EPA vials
• Inert reaction conditions - simply add sleeve,
  top and gas line
• Reaction vessels held at their top, like a round
  bottom flask
• Versatile options for heating and cooling
• Reaction mixtures easy to see
• Quick removal from heat, just pick it up
• Reflux - add on condenser when needed

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Reactor Summary

• Standard SBS microtiter array formats, compatible
  with
• Filter plates
• Filtration devices
• Liquid handling robots
• Solid addition plates
• Software for handling arrays
• Easy to clean - toss the glass, rinse with
  acetone and send it to the dishwasher
• Hood compatible works with your heater/stirrer
• Inexpensive to own and use
• Superior Design lowers complexity and cost
  relative to the competition
• Disposable glass reactors make it inexpensive to
  use
• Available parts (like the tube holder) can be
  used separately

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Reagent Addition

• Eppendorf Repeater Pipette
• Good for Repeated Additions of one Solution
• Disposable Polypropylene Syringe Barrels
• Easily adaptable to Leur fittings (needles)
• Can deliver from 0.5 uL to 5 mL
• Inexpensive and Fast (better than robots)
• Can Deliver Slurries with Modifications

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Reagent Addition

• Solids
• Isopycnic Slurry polymer based resins
• Solid addition Plates free flowing solids
• Slurries via Eppendorf Repeater Pipette
• 10 Pd on Carbon in Ethanol
• Raney Nickel
• NaHB(OAc)3 in Dichlorethane

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Analysis, Workup and Purification

• Ask any synthetic organic chemist where she
  spends most of her time and she'll say
  "Meetings!"
• And after meetings, she'll say,
• "Analysis, Workup and Purification!"
• This is where one needs to focus automation
  efforts.

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Considerations for a Chemistry Robot

• Synthetic Chemistry automation needs are very
  different from Biology or Diagnostic needs.
• Perform many different tasks occasionally
• Need quick setup
• Easy and general for all tasks
• Need robust platform
• Solvent resistant, simple maintenance
• Automation should address the more tedious tasks
• Workup extractions, filtrations, chromatography
• Analysis TLC, analytical sample prep for NMR,
  LC/MS etc.
• Reagent addition?
• Reformatting?

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Considerations for a Chemistry Robot

• Use Tecan Robots Used in HTS
• Write software from scratch.
• Hard for the programmer but done once (or seldom)
• Easy for chemists but used often
• One-to-One mapping
• Design where the Chemist only needs to specify
• Job to be done - Deck Layout (24 or 96, transfer,
  etc.)
• Heights of Source (z1) and Destination (z2)
• Volume to move
• Which wells to move
• A few optional parameters that might prove useful

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One GenericMethod Extraction

• Deck Layout
• 24 well to 24 well
• Source vertical position z1
• Destination vertical position z2
• Volume to transfer
• Wells to transfer

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One Generic Method SPE Extraction

• Deck Layout
• 24 well to 24 well
• Source vertical position z1
• Destination vertical position z2
• Volume to transfer
• Wells to transfer

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One GenericMethod TLC spotting

• Deck Layout
• 24 well to TLC plate
• Source vertical position z1
• Vertical position z2 is fixed
• Volume to transfer
• Wells to transfer

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One GenericMethod LC/MS

• Deck Layout
• 24 well to 96 well
• Source vertical position z1
• Destination vertical position z2
• Volume to transfer plus added wash
• Wells to transfer

Source
Destination
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Transfer 75/1
Speed 15-20 sec/well 6-8 min/24 well 24-32
min/96 well vs. Genesis Larger volumes Multiple
solvents Better TLC spots Smaller
Source
Destinations
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Mini-Prep 75The Software
Worktable Chooser
Z-Height volume controls
Well Chooser controls
Other controls
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Worktable Layout
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Destinations
Sources
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Z and VolumeControl
Buttons drive tip to desired Z position
Choose rack in which to set Z position Sends tip
to the rack position A1
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Syringe Speed Slider
Type in Dispense Volume
Z position
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Transfer 75/1Misc. Controls
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Mini-Prep 75Selection Control

• Select Wells to Transfer
• Click and Drag to Select Blocks
• Hold Control Key for Multiple Selects or
  Deselects
• Green shows Selected Wells
• Blue shows Selected Wells after operation

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TLC 24 Well
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TLC 24 Well
Spotting TLC plate from 24 well reactor
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Prep Tubes to 24 wells
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Prep Tubes to 24 wells
Gilson Rack adapter
Transfer from Prep tubes to FlexStore vials
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Robot Summary

• Compact, affordable liquid handling robot
• Capable of
• Extractions
• Filtratations
• Analytical Sample Prep
• TLC spotting
• Prep reconstitution
• Reagent addition and more
• Very easy to learn and use (dynamic Z control)
• Fast 15 sec/well
• Flexible and extensible

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Important ParallelThings Others Do

• Concentration
• GeneVac
• Nitrogen Streams
• Chromatography
• Isco Optix-10
• Mass Guided HPLC
• Microwave
• Personal Chem and CEM

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Other Important

• Things we know about but don't sell products
• The Synthesis-Analytical interface
• Analytical data handling of parallel formats
• And to a lesser degree
• Reagent selection
• Registration/enumeration

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Summary

• Using practical and lab tested approaches,
  InnovaSyn provides expertise and products that
  allow medicinal chemists to quickly become
  productive using parallel synthesis without the
  nasty whiplash generally associated with such
  "Paradigm Shifts".

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Acknowledgments

• Technical Contributions
• Tom Graham Programming Equipment Design
• Matt Clapham Programming
• Jose Mendoza Equipment Design
• Kent Carrow S D Machine and Tool, Inc.
  Durham, NC
• Spiritual Contributions
• Lilly RTP/Sphinx Lead Generation Group

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Reactors
Generic Reactor Block Almost all parallel
synthesis reactor blocks are based on utilizing
the bottom fourth of a tube for reactions. This
allows room for reflux within the reaction
chamber and allows one to add solvent to the tube
for extractive workup.
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Choose Chemistry

• Actually, the chemistry is more likely to dictate
  whether parallel synthesis is applicable.
• Chemistry that works