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Drew Residential School on Medicinal Chemistry. Chemical Diversity Generation and Use in Drug Discovery Philip F. Hughes InnovaSyn, LLC Chapel Hill, NC. Chemical Diversity Generation and Use in Drug Discovery. Overview Reasons, History, Economics, Definitions

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Drew residential school on medicinal chemistry l.jpg
Drew Residential Schoolon Medicinal Chemistry

  • Chemical Diversity

  • Generation and Use in Drug Discovery

  • Philip F. Hughes

  • InnovaSyn, LLC

  • Chapel Hill, NC


Chemical diversity generation and use in drug discovery l.jpg
Chemical Diversity Generation and Use in Drug Discovery

  • Overview

    Reasons, History, Economics, Definitions

  • Combinatorial Chemistry/ Parallel Synthesis

    Synthesis Methods

    split/mix, array

    solid phase, solution phase

    Equipment

    Purification Methods

    Analytical Methods

  • Conclusions


Why chemical diversity l.jpg
Why Chemical Diversity?

  • Reasons

    The biggest reason for continued interest in Chemical Diversity is the recent ability of scientists to evaluate very large numbers of molecules in biological systems.

i.e.

High Throughput Screening


High throughput screening l.jpg
High Throughput Screening

Current Screening

capacities of

2000-100,000

Samples/Day

in multiple assays

Biotechnology

Genomics

Computers

Robotics

Chemistry

synergy

Where will the Samples come from?


History l.jpg
History

  • 1990:

  • A medicinal chemists made

    2-6 compounds / month

    at $2,500-$10,000 / compound

  • Compounds were tested once in a single assay.

  • Leftover compound sent for storage


Old molecular diversity l.jpg
Old Molecular Diversity

  • Company Chemical Storage

    20,000-400,000 compounds, many similar classes, some >100 yrs. old

  • Natural Products

    large number, not clean,

    test as “mixtures”

  • Classical Medicinal Chemistry

    too slow or too expensive


New requirements l.jpg
New Requirements

  • We need to increase the compound synthesis rate by

  • 20 to 1000 fold

  • This is less than the increase in screening capacity because we’re now willing to test each compound in numerous assays


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Going Faster

  • 4 Ways to go Faster

    • Use Combinations

      • Reuse

    • Do many things at the same time

      • Parallel processing

    • Speed up the process

    • Get someone else to do it

      • Automation

      • Outsourcing


The answer l.jpg
The Answer

  • Combinatorial Chemistry

  • Combinatorial chemistry is a technology through which large numbers of structurally distinct molecules may be synthesized in a time and resource-effective manner, and then be efficiently used for a variety of applications

  • Nick Terrett

  • From the Tetnet page on Elsevier.com


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Two Major Approaches

  • Split & Mix

    “Real Combinatorial Chemistry”

  • Array Synthesis

    “Parallel Synthesis”

    “Spatially-Addressable Synthesis”

    “Matrix Array Synthesis”


Split mix l.jpg
Split & Mix

  • Originated in peptide synthesis

    Simple efficient chemistry (amides)

    Long linear sequence of reactions

    Solid Phase approaches known

# of reagents = 10

# of reactions = steps ● reagents; 5 ● 10 = 50

# of products = reagentssteps; 105 = 100,000


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Split & Mix

# of reagents = 3

# of reactions =3+ 3 + 3 = 9

# of products = 3 x 3 x 3 = 33 = 27

A Big Mixture


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Dealing with Mixtures

  • Options

    • Test as a mixture

  • Encoded Libraries

    • Tags

      • Nucleotide

      • Chemical

    • Labeled reactors


Big mixture testing l.jpg
Big Mixture Testing

  • Deconvolution generally requires repeated synthesis of smaller and smaller mixtures followed by retesting.

  • This only made sense back when screening capacity was limited.

  • www.mixturesciences.com - positional scanning


Nucleotide tags l.jpg
Nucleotide Tags

  • Beads selected based on binding to target

  • Nucleotide “code” can be defined for natural or unnatural monomers

  • Nucleotide sequence can be amplified by PCR

  • 1. S. Brenner, R. A. Lerner, Proc. Natl. Acad. Sci. USA, 89, 5381-5383 (1992)

  • 2.. M. C. Needels, d. G. Jones, E. H. Tate, G. L. Jeinkel, L. M. Kochersperger, W. J. Dower, R. W. Barrett, M. A. Gallop. Proc. Natl. Acad. Sci. USA, 90, 10700-10704 (1995)


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Chemical Tags - Pharmacopeia

  • Example: Arylsulfonamide inhibitors of Carbonic Anhydrase

  • 7 X 31 X 31 library: 6727 members (R1-R2-R3)

  • Each reagent encoded by a unique combination of 3-5 tags based on a binary code: coding 2n-1 members requires n tags

  • Tag incorporated by Rh-catalyzed carbene insertion into polymer C-H

  • Tags released from oxidatively labile linker with (NH4)2Ce(NO3)2, followed by Electron Capture GC (silylated tags)


Chemical tags pharmacopeia17 l.jpg
Chemical Tags - Pharmacopeia

  • M.H.J. Ohlmeyer, R.N. Swanson, L. W. Dillard, J.C. Reader, G. Aronline, R. Koabyashi, M. Wigler, W. C. Still, Proc. Natl.Acad. Sci. USA, 90, 10922-10926 (1993).

  • J. J. Baldwin, J. J. Burbaum, I. Henderson, M. H. J. Ohlmeyer, J. Am. Chem. Soc., 117 5588-5589 (1995).

  • Pharmacopeia’s web site www.pcop.com ECLiPS™ encoding technology

  • ICCB at Harvard iccb.med.harvard.edu/


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Chemical Tags - Pharmacopeia

1.

2.

1. Clip off compounds for testing

2. Clip off tags for analysis

(23-1)•(25-1)•(25-1) = 7•31•31 = 6727 compounds

3 + 5 + 5 = 13 tags

7+31+31=69 reagents, 69 x 2 = 138 reactions


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Labeled Reactors Radio Encoded Tags - Irori

www.irori.com Discovery Partners International


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Labeled Reactors Radio Encoded Tags - Irori

  • Similar to resin split and mix except that each reactor can is tracked throughout the synthesis. Each product is made once and each can contains only one product. Irori calls this “directed sorting”, which has been automated

  • A similar package is available from Mimotopes

www.mimotopes.com Now owned by Fisher Scientific


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Split and Mix Synthesis Points

  • 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 and analysis can be complex

  • Generally applicable to only solid phase synthetic approaches


Array synthesis l.jpg
Array Synthesis

  • Use parallel synthesis in a matrix format (8 x 12 array) - 20 reagents with 1 or 2 reactions gives 96 products


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Large Array Synthesis

  • Larger numbers of compounds are available from one scaffold or reaction scheme

  • Lay out a Super Grid

    • 72 X 72 reagents or wells

    • 9 X 6 plates = 54 plates

    • 5184 compounds

    • Chemists make multiple plates at a time

    • Need 72 + 72 reagents

Reagents

8 X 12 Plates


Array synthesis points l.jpg
Array Synthesis Points

  • 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

  • Efficiency requires at least 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 and Solid Phase Organic Chemistry

  • Definitions for the sake of discussion:

  • 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 (SPR’s) may be made using SPOC. They (SPR’s) have also made solution phase combinatorial chemistry easier.


Solid phase organic chemistry l.jpg
Solid Phase Organic Chemistry

  • Core is usually 1% crosslinked polystyrene

  • Spacer, if present, is usually a polyethylene glycol

    • TentaGelTM, or ArgoGelTM (www.argotech.com)

    • Give more solution-like reactivity with lower resin loading

  • Linker, if present, provides an orthogonal method for releasing the scaffold

  • Scaffold is the part that you’re interested in doing chemistry on and releasing at the end of the synthesis



An example l.jpg
An Example

H. V. Meyers, G. J. Dilley, T. l. Durgin, T. S. Powers. N. A. Winssinger, H. Zhu, M. R. Pavia, Molecular Diversity,1,13020 (1995)



Solid phase organic chemistry30 l.jpg
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)

    • Can’t use Solid Phase Reagents (SPR)

    • Modified kinetics (generally slower, greater rate distribution, all sites not equal)

    • Requires new analytical methods

    • Requires linking chemistry (limits reaction conditions, constrains product structure)


Solution phase organic chemistry l.jpg
Solution Phase Organic Chemistry

  • More compounds means less time per compound

  • This requires:

    • Good generalized procedures

    • Short synthetic sequences

    • High yield reactions

    • Stoichiometric addition of reactants

    • Parallel or high throughput purification methods


Solution phase organic chemistry32 l.jpg
Solution Phase Organic Chemistry

  • Multiple Component Condensation Reactions

Armstrong, R.W., Combs, A.P., Tempest, P.A., Brown, S.D., & Keating, T.A. Account. Chem. Res., 29, 123-131 (1996).


Solution phase organic chemistry33 l.jpg
Solution Phase Organic Chemistry

3072

Compounds

Single isomer

> 95%

IC50 = 420 nM FTase

Competitive Inhibitor

iterate

IC50 = 1.9 nM FTase

for enantiomer shown

Shinji Nara, Rieko Tanaka, Jun Eishima, Mitsunobu Hara, Yuichi Takahashi, Shizuo Otaki, Robert J. Foglesong, Philip F. Hughes, Shelley Turkington, and Yutaka Kanda. J. Med. Chem.; 2003, 46, 2467-2473


Solution phase organic chemistry34 l.jpg
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 (SPR’s) is possible

    • No linkers required, less excluded chemistry

    • Requires development of parallel workup and purification methods

  • Called Parallel Synthesis or Rapid Parallel Synthesis (RPS)


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Trends over the Last Decade

Sld P S&M

Sld P Array

10,000+

Solu P Array

2004

# of

Compounds

1000+

Solu P Array

1996

Classical Organic Synthesis

0

time

Solution Phase Array or Parallel Synthesis now dominates

Dev. times for solid phase


Equipment for solid phase organic chemistry l.jpg
Equipment for Solid Phase Organic Chemistry

  • Split & Mix

    Standard labware with gentle stirring

  • Array

    Geyson Pin Approach

    Bottom filtration

    Top filtration

    Little stuff

    Big stuff


Geysen pin method l.jpg
Geysen Pin Method

Resins attached to pins in an 8 x 12 array format

Reagents or wash solvents in a 96 deep-well plate

Drop it in to run reactions or wash resins

Kits available from Mimotopes

www.mimotopes.com


Equipment for solid phase organic chemistry38 l.jpg
Equipment for Solid Phase Organic Chemistry

Problem: How do you put 24-96 of these together?

Bottom Filter

Top Filter


Original sphinx reactor l.jpg
Original Sphinx Reactor

  • Solid Phase Chemistry Reactor

    Plate in a Plate Clamp

Strip Caps used to seal reaction after reagent addition

Plate removed from clamp for resin washing

Plate Bottom acts as a 96-way valve

H.V. Meyers, G.J. Dilley, T.L. Durgin, et al Molecular Diversity1995, 1, 13-20


Commercial apparatus for solid phase l.jpg
Commercial Apparatus for Solid Phase

Big Stuff

  • Argonaut

    • Quest 210

    • Nautilus 2400

    • Trident

  • Bohdan Ram

  • Tecan Combitec

  • Advanced Chemtech 496

  • Myriad Core

  • All Discontinued

  • Big stuff is a bad idea.

Little Stuff

FlexChem

www.robsci.com

www.scigene.com

MiniBlock

www.bohdan.com

www.Autochem.com

Polyfiltronics/Whatman

www.whatman.com

Charybdis Technologies

www.spike.cc


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Parallel Solution Phase Organic Synthesis

  • Equipment – An Array of Vessels

    • Heating and cooling

    • Mixing

    • Inert Atmosphere

    • Access for addition and sampling

  • Methods

    • Reactants and reagents added as solutions or slurries

    • Run at equimolar scale

    • Separate the reaction from the workup


Equipment for parallel solution phase organic synthesis l.jpg
Equipment for Parallel Solution Phase Organic Synthesis

  • One at a time Synthesis

  • Parallel Synthesis


Equipment for parallel solution phase organic synthesis43 l.jpg
Equipment for Parallel Solution Phase Organic Synthesis

Generic

Reactor Block


Equipment for solution phase organic synthesis l.jpg
Equipment for Solution Phase Organic Synthesis

  • Reactor Blocks


Equipment for solution phase organic synthesis45 l.jpg
Equipment for Solution Phase Organic Synthesis

  • MicroWave

Biotage

http://www.personalchemistry.com/

http://cemsynthesis.com


Solution slurry addition l.jpg

eppendorf

4

3

5

2

1

Solution/Slurry 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


Solid addition l.jpg
Solid Addition

  • Solid addition plates/Vacuum systems

  • Solid as a slurry

    • 10% Pd on Carbon in Ethanol

    • NaHB(OAc)3 in Dichlorethane

    • Resins as isopycnic slurries


Purification methods l.jpg
Purification Methods

  • Solid Phase

    • Wash exhaustively

    • product dependent cleavage

  • Solution Phase - Parallel Purification

    • Extraction

      • liquid-liquid, acid/base

      • SPE, scavenging resins

      • Fluorous Synthesis

    • Chromatography


Scavenging resins l.jpg
Scavenging Resins

S. W. Kaldor, J. E. Fritz, J. Tang, E. R. McKinney, Biorganic & Med. Chem. Lett.., 6,3041-3044 (1996).


Fluorous synthesis l.jpg
Fluorous Synthesis

Fluorous (C6F12) Phase

Aqueous Phase

Halocarbon (CH2Cl2) Phase

D. P. Curran, M. Hoshino, J. Org. Chem., 1996,61, 6480-6481.

D. P. Curran and Z. Luo, Fluorous Synthesis with Fewer Fluorines (Light Fluorous Synthesis): Separation of Tagged from Untagged Products by Solid-Phase Extraction with Fluorous Reverse Phase Silica Gel, J. Am. Chem. Soc., 1999, 121, 9069. http://fluorous.com


Liquid handling robots a primer l.jpg

10 mL Loop

Tees

Robot

Arm

6-Way Valve

Tip

X

System Solvent

Y

Z

Syringes

Liquid Handling RobotsA Primer


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Purification Methods

  • Filtration

    • Salt Removal

    • Covalent and Ionic Scavenging Resin Removal

  • Extractions

    • Liquid-Liquid

    • SPE - Solid Phase Extraction

  • Chromatography

    • Silica

    • C18

    • Fluorous Silica

Use Parallel Filtration

and a Liquid Handling Robot


Filtration l.jpg
Filtration

  • Salt Removal

  • Covalent and Ionic Scavenging Resin Removal

Robot Tip

Filter plate

Source plate

Destination plate


Extractions l.jpg
Extractions

  • Liquid-Liquid

    1. Positional Heavy Solvent Extraction

    2. Positional Light Solvent Extraction

    3. Liquid Detection Light Solvent Extraction


Chromatography and spe l.jpg
Chromatography and SPE

  • Silica Gel

  • Fluorous Silica Gel

  • C18

  • Ion Exchange

1. Dissolve Samples in a suitable solvent

2. Transfer to little chromatography columns

3. Elute clean products and/or collect fractions


Chromatography example l.jpg
Chromatography Example

  • Cyclic Urea Plate, wells 1-48, Before and After Filtration through Silica gel


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Commercial 24 & 96-wellFilter Plates

  • Varian http://www.varianinc.com

  • Oros technologies http://www.oroflex.com

  • Robbins Scientific http://www.robsci.com

  • Polyfiltronics http://www.polyfiltronics.com

  • Whatman http://www.whatman.com

  • Spike International http://www.spike.cc


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Commercial Robotics

  • Robots

    • TECAN http://www.tecan-us.com

    • Hamilton http://www.hamiltoncomp.com

    • Gilson http://www.gilson.com

  • Custom solutions

    • Chemspeed http://www.chemspeed.com

      • Complete reaction stations

    • AutoChem http://www.mtautochem.com

      • weighing, extraction, transfers

    • InnovaSyn http://www.innovasyn.com

      • extraction, transfers, TLC spotting

    • J-KEM http://www.jkem.com


High through put prep hplc l.jpg
High Through-PutPrep HPLC

  • Systems based on UV and/or ELSD

    Biotage

    Gilson

    Argonaut

    Isco

  • Systems based on Mass Spect

  • MicroMass, PE Sciex, Shimadzu, Agilent


Analytical methods l.jpg
Analytical methods

  • Solid Phase - few high throughput methods

    • NMR - gel phase, MAS

    • IR - works well

    • MS - laser assisted removal and ionization

    • elemental analysis - must analyze starting materials

  • Solution Phase - some high throughput methods

    • TLC - ideal for parallel analysis

    • MS - ion spray, 45 sec./sample, reports at 2 sec./sample

    • NMR - high throughput with flow probes 2 min./sample

    • HPLC, LC-MS 5 min./sample

  • The challenge is not so much to collect the data as to analyze it.


Robotic tlc plate spotting l.jpg
Robotic TLC Plate Spotting


Example tlc plate l.jpg

C

B

D

A

Example TLC Plate

  • Some Pertinent Points

    • Analyze an entire plate (96 compounds) at once

    • Trends are easy to spot

      • Note similar impact of substituent change

      • Common impurities

      • Common by-products

      • Can Spot Across or Down to See Trends

    • Non linearity of detection

    • No structural information


Mass spectroscopy l.jpg
Mass Spectroscopy

  • Mass Spectrometers used in Combinatorial Labs

    • Use an Ion Spray technique (ES or APCI) to allow flow injection analysis (FIA)

    • Auto Samplers sample from multiple 96 well plates

    • Use quadrapoles for mass filters

    • Have data analysis and reduction packages for matrix analysis

    • Can run samples at < 1 min. each

    • LC/MS becoming much more routine (5 min. each)


Analytical data analysis lc ms l.jpg
Analytical Data AnalysisLC/MS

MicroMass Diversity Browser

Lilly RTP Analytical Viewer


Analytical data analysis nmr l.jpg
Analytical Data AnalysisNMR

ACD’s SpectView

SLAVA

SLAVA


Trends l.jpg
Trends

  • 1. With higher screening throughput there is a trend away from making or testing mixtures.

  • 2. With better purification methods, SPOC no longer dominates combinatorial chemistry.

  • 3. Everyone is demanding purer products and more material with better characterization.

  • 4. Equipment complexity is dropping as we learn to be clever rather than over-engineer. There are more commercial options though big machines are going away.

  • 5. The methods of Parallel Synthesis are slowly finding their way into all aspects of synthetic chemistry.

  • 6. Handling data (registration, analysis, results) remains a major challenge.

  • 7. Combinatorial Chemistry/ Parallel Synthesis is here to stay.


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Conclusions

  • By application of robotics, computers, clever engineering and chemistry, the methodology now exists to synthesize, with reasonable purity and yield, medicinally relevant organic molecules at 100 to 10,000 times the rate possible just 10 years ago. The field of Combinatorial Chemistry/ Parallel synthesis is evolving and melding with classical Medicinal Chemistry.


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Further Information

www.combichem.net

www.combichemlab.com

www.5z.com

www.combinatorial.com

www.netsci.org

www.innovasyn.com

www.google.com


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Archiving TLC Plates

  • UV Images

    • Captured using a UV Light Box with a Visible Camera

  • Visible Images

    • Captured using a Scanner

  • All Images Stored on Disk and Printed for Notebook storage