1 out of 4000 candidates becomes a drug - UEF...1 out of 4000 candidates becomes a drug IND NDA 0 712years probability Drug Discovery Drug Development 11 March 2003 Ari Koskinen Note:

11 March 2003 Ari Koskinen

Solid Phase Organic ChemistrySolid Phase Organic Chemistry-- Dr. SPOCK?Dr. SPOCK?


1 out of 4000 candidates becomes a drug1 out of 4000 candidates becomes a drug

IND

NDA

0 7 12 years

probability

DrugDiscovery

DrugDevelopment


Note: Ethical pharmaceuticals only. Expenditures worldwide by U.S.-owned research-based pharmaceutical companies

C&EN January 17, 2000, Food & Drug Administration,Pharmaceutical Research & Manufacturers of America: PhRMA Annual Survey 2000.

New Chemical Entities vs. R&D Expedinture

0

10

20

30

40

50

60

86 87 88 89 90 91 92 93 94 95 96 97 98 99

Num

ber

appr

oved

by

FDA

0,00

0,10

0,20

0,30

0,40

0,50

0,60

0,70

4,8 5,5 6,6 7,2 8,4 9,811,5

12,713,5

15,216,6

18,721,0

24,0$ billions

$ / N

o.

R&D Spending $billions

New molecularentities approved byFDARatio: $ / No.


New Drug DevelopmentNew Drug Development


Of the $ 360 million per product,Of the $ 360 million per product,the the PharmaPharma industry spends onindustry spends on

R&D Stage % of spendinga % of employeesb

Synthesis/extraction 11.0 12.9

Biological screening/pharmacological testing

16.0 18.3

Toxicology/safety 6.0 7.8

Dosage formulation 9.6 11.6

Clinical evaluation 34.5 24.3

Process development formanufacturing/ qualitycontrol

9.6 10.3

Regulatory 3.8 4.8

Other 9.4 10.0

a Company financed R&D in US based on 1995 figures totalling $ 11.8 bnb US scientific and professional personnel totaling 34, 784 employeesSource: Pharmaceutical Research & Manufacturers of America, Industry Profile 1997


The top five bestThe top five best--selling antibiotics selling antibiotics (1997 worldwide sales)(1997 worldwide sales)

MedAdNews 1998, 17, 18 - 23.


Diversity of Drug StructuresDiversity of Drug StructuresNHS

O CO2H

O

O

O

OHOMeHO

O OH

OMe

OHONMe2

OO

O

R H

OH

O

NH

O O

OF

N

HN

S NO

MeO

OMe NH

O

F3C

NH

N

NH

CN

S N

HN

N

NO

Cl

O HN

NN

O

NN

HONH

O

OHN

O NHS

H

HNH

NH

NO2

SO

NMe2

NH2

ClCl

N

OH OHCO2H

NH

O

F

Captopril(anti-hypertensive)

Clarithromycin(antibiotic)

R = H: MevacorR = Me: Zocor

(treatment of high cholesterol)Paxil

(psychoterapeutic)

Prilosec(antispasmodic)

Prozac(antidepressant)

Tagamet(anti-ulcer) Valium

(tranquilizer)

Viagra(treatment of impotence) Viracept

(treatment of AIDS)

Zantac(anti-ulcer) Zoloft

(psychoterapeutic)

Atorvastatin(anticholesterol)


MaitotoxinMaitotoxin

O

O

O

OH

MeMeOHMe

MeOH OSO3NaO

O

O

OHOH

OHHO OH

HO

OH

NaO3SOMe Me

OHO

O

O

O

OO

OH

OHOOH

OHOH

HO

OH O

OH OH

O

OH

OH

HO

O

OO

OH

HOMeMe

MeO

O

O

O

OHO

O

O

O

O

O

Me

Me

MeMe

MeMeMe

O

OO

OHO

Me

Me

Me

Me

OH

Me

LD50 50 ng/kg, mouse (ip)MW 3422 DaIsolated from Gambierdiscus toxicusCiguateric food poisoning


Natural Products as Drug LeadsNatural Products as Drug Leads

Cl

HOCl

OMe

Me

O

OO

O

O

Me OMe

OO

O

O O

O

MeO O

O

O

O

O

O

O

O

OO

O

HO

O Me

OH

Me

MeNO2

HO

Me

MeOH

Me

OH

OMe OH

OMeOH

Me

A1 A2

A

B C D F H

OHO

O O O

O

Me

O

Me

OOO

HN

Me

Me

OH

Me

Me

H

H

H H

OH H

H

H

AB

C DF

H

I

BrOMe

OOH

OMe

N

O

O

O

O

O

N

O

O

OH

OH

O

O

Me

MeO

Me

MeOO

NHO

O

Cl

H OHO

MeO

Me

Me

H

Everninomicin 13,384-1

E G

E G

Azaspiracidcausative agent for 1995 human poisonings by contaminated Irish mussels

Mytilus edulis

1

16

242933

4346

Phorboxazole A

5

9

Callipeltoside Ainhibits proliferation of KB and P388 cells

protects cells infected with HIV


Some Clinically Important Natural ProductsSome Clinically Important Natural Products

TaxolTaxolPromising anti-cancer drug

ThienamycinThienamycinProduced by TOTAL SYNTHESIS

by Merck (Imipenem)

MeONMe2 OH H

N

OH O

N

O

O

OOH

H2O3PO

OH OMeOH

CN

LL--659,699659,699 (a lipstatin analogue)inhibitor of HMG-CoS synthase

Calyculin ACalyculin AProtein phosphatase inhibitor

OOH

O

OHOAcO

OBz OAcH

OH

BzHN O

NO

OH

CO2H

SNHAc

H H

OO

OHHO2C


Natural Product Inhibitors of Protein Natural Product Inhibitors of Protein Phosphatases 1 and 2APhosphatases 1 and 2A

NH

OO

HN

ONH

Me

N

CH2Me

NHMe

OMe

Me Me

CO2H

NH

H2N CO2HO O

NH HN Me

Me

OMe

ONH

O

HN

ONH

Me

MeOMe

Me Me

NH

H2N CO2HO

CO2H

N

MeN

Me

NHO

OH

MeONMe2 OH H

N

OH O Me

N

O

OMe

OOH

MeMe

H2O3PO

Me OH OMeOH

MeMeMe

Me

CN

OOHH

Me

OHO2CH

Me OH

Me

O

O

Me

OO

MeOH

H

H HHOH

OH

OkadaicOkadaic acidacid Calyculin ACalyculin A

NodularinNodularin MicrocystinMicrocystin--LRLR


High Throughput ScreeningHigh Throughput Screening! Plant extracts! Marine natural

products! Invertebrate natural

products! Compound libraries! Structure based

design! Recombinant

methods! Peptide libraries! Peptidomimetic

libraries


Drug Development ParadigmsDrug Development Paradigms

in vivo

in vitroor in vivo

in vitro

in vivo

designdesign

Studies on pathophysiology

Clinical/preclinical Observations

Disease gene

Transgenic animals

Traditional Approach

Rational Approach

Disease model

Validated target LEAD

LEAD


Drug Development ParadigmsDrug Development ParadigmsTARGET IDENTIFICATION

LEAD GENERATION

LEAD OPTIMIZATION

DRUG CANDIDATE

Generalcombinatoriallibraries

Biasedcombinatoriallibraries

Structuralchemistry


Role of Combinatorial Chemistry in Modern Role of Combinatorial Chemistry in Modern Drug DiscoveryDrug Discovery

General combinatorial libraries

Biased combinatorial libraries

Structural chemistry

Time

$


Trends in Synthetic MethodologyTrends in Synthetic Methodology

PERIOD TREND OBJECTIVE/OUTPUT

1950-1960 Classical synthesisof natural products

Target conquestMechanisms, Spectroscopy

1970-1980 Multistep, strategyand transformationbased synthesis

Stereo/enantiocontrolSynthetic methods

1990- Designed molecules Selectivity, RecognitionFunction, Intelligence

Hardware

Software


Combinatorial Information

! Is constitutionally! energetically essentially identical

! but structurally different information.! (e.g. DNA, RNA, peptides?, proteins?,...)

EschenmoserEschenmoser, A. , A. ESOC IXESOC IX, Warsaw, Jun 19, 1995., Warsaw, Jun 19, 1995.


Chemical DiversityChemical DiversityLibrary EntitiesUnits

8 000

160 000

3 200 000

203

204

205

Units Library Entities

1 Million

100 Million

10 Billion100 5

100 3

100 4

Units Library Entities

1000 3

1000 4

1000 5

1 Trillion

1 Billion

1 Quadrillion

Basis set of 20(e.g. natural amino acids)

Basis set of 100(e.g. carbohydrates)

Basis set of 1000(e.g. synthetic building blocks)

The number of different chemical entities,N = bx, where x = the number of steps,

and b = number of different building blocks.

The problem of combinatorial synthesisis not that of making compounds, butthat of finding ways to selectand identify the compounds:

One must be able to extract the informationmade available by library screening.


Spectrum of Molecular DiversitySpectrum of Molecular Diversity

1012 1010 108106 104 102 100

Number of molecules

Lead Identification Chemical AnalogingFineTuning

Recombinant Peptide Diversity

Noncoded Synthetic LibrariesEncoded Synthesis Libraries

Recursively Factored Libaries

Spatially Addressable Libraries

MPS

Diversomers

Serial Medicinal Chemistry


Two Major StrategiesTwo Major Strategies

! Broad Screening

! huge library size! broadest structural diversity! no special initial structure goal! any building blocks

! undefined order of reactions! flexible synthetic strategy! site of tether not crucial! ligand possibly uncouplable! single selection evolution

! ChemicalAnaloging/Optimization

! modest library size! relatively narrow structural diversity! specific structural goal! specific retrocombinatorial building

blocks! specific order of combination! well defined synthetic strategy! tether crucial - build in redundancy! ligand should be releasable! cumulative selective evolution


Combinatorial ChemistryCombinatorial Chemistry• solid-phase organic chemistry (SPOC)• combinatorial synthesis• structure elucidation based on deconvolution and tagging• structure-diversity• automation Reviews:

Special Issue: Acc. Chem. Res. 1996, 29, # 3 (March).Hermkens, P.H.H.; Ottenheijm, H.C.J.; Rees, D. Tetrahedron 1996, 52, 4527-4554.

Früchtel, J.S.; Jung, G. Angew. Chem., Int. Ed. Engl. 1996, 35, 17-42.Lowe, G. Chem. Soc. Rev. 1995, 24, 309.

Ellman, J. Chemtracts: Organic Chemistry 1995, 8, 1-4.Pirrung, M.C. Chemtracts: Organic Chemistry 1995, 8, 5-12.

Czarnik, A.W. Chemtracts: Organic Chemistry 1995, 8, 13-18.Mitscher, L.A. Chemtracts: Organic Chemistry 1995, 8, 19-25.

Dolle, R.E.; Nelson, K.H. J. Combinator. Chem. 1999, 1, 235-282.


Combinatorial Chemistry PublicationsCombinatorial Chemistry Publications

0200400600800

100012001400

#

1985

1987

1989

1991

1993

1995

1997

Year

Combinatorial Chemistry

PatentsPublications


Biological Methods for Displaying Biological Methods for Displaying Chemical DiversityChemical Diversity

• Synthetic oligonucleotides to create genetic mutants since 1970’s.• Insert oligonucleotide cassettes: mutant libraries up to 1011 members.• Peptides on Phage Particles

◊ N-terminal expression; secreted to periplasmic compartment; anchored in the membrane

◊ mainly for protein and protein domain expression; noted to be acceptable for epitope library generation, too.

• Peptides on Plasmids◊ Peptides attached to the C-terminus of fusion proteins: free carboxy

termini◊ Processing of the polypeptide restricted; LacI fusion proteins: cytoplasm

of host.◊ Couple with peptidyl amino monooxygenase: C-terminal amides;

suggested for G-protein receptor screens.


Biological Methods for Displaying Biological Methods for Displaying Chemical DiversityChemical Diversity

• Peptides on Polysomes◊ Stall the ribosomes on the mRNA; nascent peptides still

linked to their encoding RNA, which is recovered, converted to cDNA, amplified by PCR for identification and production of the peptide.

◊ Can be coupled with phage display system.◊ DNA library of 1012 decapeptides has been generated.◊ Larger production systems (up to mL volumes) can

provide library sizes 1014-1015.

Gallop, M.A.; Barrett, R.W.; Dower, W.J.; Fodor, S.P.A.; Gordon, E.M. J. Med. Chem. 1994, 37, 1233-1251.


Synthetic Methods for Displaying Synthetic Methods for Displaying Peptide DiversityPeptide Diversity

! Multipin synthesis! 96-(384)well plates, direct ELISA etc.

! Epitope mapping, PEPSCAN technique! Tea-bag method

! polypropylene bags! epitope mapping, peptide-hormone structure-function analysis,

protein conformational mapping! Coupling Amino Acid Mixtures

! Relative rate constants! Nontraditional Supports

! Cellulose, paper disks, cotton fragments


Solid Phase Organic SynthesisSolid Phase Organic Synthesis

Kawana, M.; Emoto, S. Tetrahedron Lett. 1972, 4855-4858.

Crowley, J.I.; Rapoport, H. Accts. Chem. Res. 1976, 9, 135-144.

Scrambled product must arise through intraresin reactions.

Intraresin reactions occur even at resin loadings of 0.5 % (0.05 mmol/g resin!)

1. MeMgI2. H2O3. KOH4. H+

Atrolactic acid

O

OO

O

OPh

Ph

PhOO

Ph

OH

CO2H

Me

*

***

Autocleaved esterResin bound ester

OO

O

OO

OEt3C

CH2OCO

(CH2)5 CO

O CEt3


Combinatorial Library:Combinatorial Library:Split Synthesis MethodSplit Synthesis Method

Bead

A B C

A B C

POOL

A

A

B

A

C

A

A

B

B

B

C

B

A

C

B

C

C

C

A B CPortioning-mixing

Furka, A. et al. Int. J. Pept. Protein Res. 1991, 37, 487-493.Furka, A. et al. Bioorg. Med. Chem. Lett. 1993, 3, 413-418.

Split SynthesisHruby, V.J. et al. Nature, 1991, 354, 82-84.

Divide, Couple and RecombineHoughten, R.A. et al Nature 1991, 354, 84-86.


Combinatorial SynthesisCombinatorial Synthesis

Reviews:

Dolle, R.E.; Nelson, K.H. J. Combin. Chem. 1999, 1, 235-282.Gallop, M.A.; Barrett, R.W.; Dower, W.J.; Fodor, S.P.A.; Gordon, E.M. J. Med. Chem. 1994, 37, 1233-1251.Gordon, E.M.; Barrett, R.W.; Dower, W.J.; Fodor, S.P.A.; Gallop, M.A. J. Med. Chem. 1994, 37, 1385-1401.Dower, W.J.; Fodor, S.P.A. Annu. Rep. Med. Chem. 1991, 26, 271-280.Moos, W.H.; Green, G.D.; Pavia, M.R. Annu. Rep. Med. Chem. 1993, 28, 315-324.Mitchinson, T.J. Chem. Biol. 1994, 1, 3-6.


Construction of an Encoded Synthetic LibraryConstruction of an Encoded Synthetic LibraryTags should have high information content, be amenble to high sensitivity detection and decoding, and must be chemically orthogonal to the oligomer protocol.

Single-stranded oligonucleotides, coupled with PCR amplification: 8.2 x 105 synthetic peptides.

also: Lerner, R.; et al PCT Appl. WO 93/20242.Nielsen, J. et al. JACS 1993, 115, 9812-9813.

Tags a, b, and c are attached to the same beads as the growing oligomer chain. The overall structure of the ‘hit’ oligomer can then be read from the tag information.

Dower, W.J. et al. PCT Appl. WO 93/06121.Needels, M.N. et al. PNAS 1993, 90, 10700.

CBA

POOL

CBA

a b c

a b c

cb aaa a

A

A

A

B

A

C

b c

B CA

a

cbb b ba

B

C

B

B

B

A

ccc b

C

C

C

B

C

A

c a


Synthesis of Encoded Synthetic LibrariesSynthesis of Encoded Synthetic LibrariesDdzFmoc

MIX

To each portion:- deprotect Fmoc- couple binding monomer(Bn)- deprotect Ddz (or Moz)- couple coding monomer(C n)

C1B1 C2B2 C3B3

Repeat

DdzFmoc HN

OFmoc-NH NH-Moz

O

MeO

OMe

Resin

=

Natural amino acids were usedto code for peptoid sequences.

Zuckermann, R.N. J. Am. Chem. Soc. 1993, 115, 2529-2531.


Synthesis of Binary Encoded Synthesis of Binary Encoded Synthetic LibrariesSynthetic Libraries

After assembly, and selection of beads,photolysis releases the haloarene tagsfor ECGC analysis. High sensitivity(up to ~106 member libraries).

A+

T1

B+

T2

B

T2

A

T1

C+

T1+T2

C

T1 T2

POOL

A

T1

T3

T4

C

T4

B

C

T2 T3

C

T1

T2

T3

T4

C

T2

B

B

T4

C

T1

T2

T4

B

A

T1

T4

B

T3

T2

B

A

C

T1

T2

T3

A

A

T1

T3

A

Repeat with T3, T4, and T3+T4

Ohlmeyer, M.H. et al PNAS 1993, 90, 10922-10926.Borchardt, A.; Still, W.C. J. Am. Chem. Soc. 1994, 116, 373-374.

Ar =

Pholabile Linker Electrophoric TagCl H

F

HCl

Cl H

Cl

HCl

Cl Cl

Cl

ClCl

HO2C

NO2

OO

O

(CH2)nO

Ar


Spatially Addressable Parallel Spatially Addressable Parallel Chemical SynthesisChemical Synthesis

Fodor, S.P.A.; Read, J.L.; Pirrung, M.C.; Stryer, L.; Yu, A.T.; Solas, D. Science 1991, 251, 767.Jacobs, J.W.; Fodor, S.P.A. Trends Biotechnol. 1994, 12, 19-26.

hν

NHX

NHXX

NHXNH

hν

NHX

NHAA

NHXNH

X X

BD

ACC

ADB

E E F F

RepeatBX

AXX

AXB

Couple

X-B

Mask 2

Couple

X-ADeprotect NHX

NHAA

NHXNH

X XMask 1

NHX

NH2NH2

XNH


Spatially Addressable Chemical LibrariesSpatially Addressable Chemical Libraries

Fodor, S.P.A.; Read, J.L.; Pirrung, M.C.; Stryer, L.; Yu, A.T.; Solas, D. Science 1991, 251, 767.Jacobs, J.W.; Fodor, S.P.A. Trends Biotechnol. 1994, 12, 19-26.

Pirrung, M.C.; Read, J.L.; Fodor, S.P.A.; Stryer, L. U.S. Pat 5,143,854, 1992.Holmes, C.P.; Fodor, S.P.A. In Innovation and Perspectives in Solid Phase Synthesis and Complementary

Technologies; Epton, R., Ed., Intercept, UK, 1994.


LinkersLinkers

CH2Cl

O CH2OH

PEGHN C

O H2C O CH2OH

O

OH OMe

OMe

Chloromethyl resin RCOOH, RCOOMe, RCH2OH, ROH

Wang resin

NovaSyn TGA

Rink resin

RCO2H, ROH

RCO2H, ROH

RCO2H, ROH, RCONR'2

Linker Resin Cleavage to give:


LinkersLinkers

O

FmocHN OMe

OMe

Trityl resins RCO2H, ROH, RSH, RNH2, etc

O

FmocHN OMe

OMe

Rink amide RCONHX

RCONHXNovaSyn TGR HN

OPEG

Linker Resin Cleavage to give:

Cl

X


Peptides and Peptides and PeptoidsPeptoids

N

R1

NH O R3

N NH

H O R2 H O R4

NR1

N

ONR3

NO R2 O R4

Peptides

Peptoids


Peptides andPeptides and PeptoidsPeptoids

! A. “Full Monomer” Oligomer Synthesis

! B. “Sub-Monomer” Oligomer Synthesis

Zuckermann, R.N.; Kerr, J.M.; Kent, S.B.H.; Moos, W.H. J. Am. Chem. Soc. 1992, 114, 10646-10647.

Deprotect Couple ONR1

ONFmoc

R2

ONH

R1ONFmoc

R1

Acylation Alkylation ONR1

ONH

R2

ONR1

OBr

ONH

R1


Peptides and Peptides and PolycarbamatesPolycarbamates

N

R1

NH O R3

NNH

H O R2 H O R4

O NH O

O NO

O R1 H

R2

N

O

H

R3

Polycarbamates

Peptides


Peptides andPeptides and PolycarbamatesPolycarbamates

Schultz, P.G. et al. Science, 1993, 261, 1303-1305.

Linker Linker Linker

n+1

a or b [repeat a ,b]n

then c,dN O

ONHAc

RHN O

ONH2

RHNH2

REAGENTS: a) p-Nitrophenyl carbamate monomer, HOBt, DIPEA, NMP;b) piperidine, NMP or hn; c) Ac2O, NMP; d) TFA, Et3SiH.

a or b

c

MeOMeO

O NH

NO2 O RO O

O NO2

MeOMeO

O NH O

NO2 O ROH

MeOMeO

O NH

NO2 O ROH

REAGENTS: a) BH3, THF; b) DCC, HOSu, HOBt, then NABH4, EtOH;p-Nitrophenyl chloroformate, CH2Cl2, pyridine.


PeptidylPeptidyl PhosphonatesPhosphonates

Campbell, D.A.; Bermak, J.C. J. Org. Chem. 1994, 59, 658-660.Campbell, D.A. J. Org. Chem. 1992, 57, 6331-6335.

ProteaseSubstrate

Peptidyl PhosphonateProtease Inhibitor

NOH P2

NNH O

N

P1'N

O P3'

NNH

H O P1 H O P2' H OP3

H

NOH P2

NNH

PO

P1'N

O P3'

NNH

H O P1 O P2' H OP3

HOHO

+

DIADP(4-ClPh)3

DIPEA

0.5 - 20 h> 90 %

HO

P1'

NH

O O

O N

P1

PO

OMe

H

O2N

O

P1'

NH

OO

O N

P1

P OHO

OMe

H

O2N


PeptidylPeptidyl PhosphonatesPhosphonates

Campbell, D.A.; Bermak, J.C. J. Org. Chem. 1994, 59, 658-660.Campbell, D.A. J. Org. Chem. 1992, 57, 6331-6335.

Synthesis of NPEOC-αααα-aminophosphonic acids

Synthesis of Fmoc-αααα-hydroxycarboxylic acids

Pb(OAc)4

DMFTiCl4P(OMe)3

1) aq. KOH2) H2, Pd/C

NPEOC-Claq. Na2CO3

N PH

P1

O

OMeOHO

OO2N

H2N P

P1

O

OMeOH

N PH

P1

CbzO

OMeOMeN OAc

H

P1

CbzNOH

OHP1

Cbz

NaNO2, H+1) TIPS-Cl, NMM, pyr2) Fmoc-Cl, NMM

3) TBAF, THFOH

P1'

OFmocOOH

P1'

OHOOH

P1'

OH2N


Hydroxylamine ResinHydroxylamine Resin

νmax 1792 and 1743 cm-1

Tetrahedron Lett. 1997, 38, 7233-7236

Ph

PhCl

N

O

O

HO

Ph

PhN

O

O

O

Ph

PhNH2O

NEt3/DMF

N2H4/THF


Succinyl Succinyl Amide LibraryAmide Library


O

O

O Ph

PhNH

O

Ph

PhNH2O

THF

OOH

O

RNH2, DCC/HOBt

DMF, rt

Ph

PhNH

O

ONHR

O

HCO2H/THFNH

HO

ONHR

O

PhOMe

O

OMe

O

Ph


Peptidic and Peptidomimetic LibrariesPeptidic and Peptidomimetic Libraries

Ph

PhO NH2 HO N

H

OH N

O

O

O

O

a, b, c

10

4 11

R1

R2 HO N H

OH N

OR2

R1

R1

12

+

OMe OMePh Ph

Ph

OO

Me Ph BnPh

a b c dentry

R1 =

R2 =

Compound 10, 11, 12

a) 60 °C, 6 h, THF; b) (S)-phenylethylamine or amino acid eater hydrochloride/ triethylamine, HOBt, DCC (5-fold excess), DMF, 6 h; c) HCO2H/THF (1:3), 1 h

Reagents and conditions:

Scheme 3Tetrahedron Lett. 1997, 38, 7233-7236


Crude NMRCrude NMR

(ppm)

1 2 3 4 5 6 7 8 910 0

10

20

30

40

50

60

70

80NH

OHO

HN

OOMe

O

N

O

O

OH



Sulfonamido Sulfonamido Hydroxamic AcidsHydroxamic Acids

SolutionSolution

Solid phase - combinatorialSolid phase - combinatorial

CH2(CO2H)2, EtOH

1) ArSO2Cl, NaOH, ∆2) SOCl2, CH2Cl23) NH2OH.HCl, NaOHO

R H

R

H2N

O

OH

R

N

O

NOH

H

H

SO OAr

NH4OAC, reflux

OH O N

O

O

O NH2i ii

O N

O

H

RN

HO N

O

H

RN

iii

iv

H

SO

O

Ar

H

SO

O Ar

Wang resin


Alcohols on Solid SupportsAlcohols on Solid Supports

Coupling yields high; generally ca 70-80 %.

Overall yields for resin cleaved carbamatesin the 47-86 % range (after chromatography,based on initial resin loading of alcohol).

Thompson, L.A.; Ellman, J.A. Tetrahedron Lett. 1994, 35, 9333-9336.

Kick, E.K.; Ellman, J.A. J. Med. Chem. 1995, 38, 1427-1430.

+Dimethylacetamide

rt, 16 h

O O-Na+ Cl OO

PPTS, ClCH2CH2Cl

HIV-1 Protease inhibitor

HN

Ph

OHNR2

R1O

OO

N3

Ph

OOTs

OON3

Ph

OHOTs

OO


Combinatorial Synthesis ofCombinatorial Synthesis of BenzodiazepinesBenzodiazepines::22--AminobenzophenonesAminobenzophenones

Cl O

RA

1) Pd(0)

2) NaSH, MeOH/H2O

KHMDS

NH

OO

O

NH2

O

RA

NH

OO

O

NO2

SnMe3

NH2

NO2

SnMe3O

O

NC OO+

NO2

SnMe3HO

OONC

X

O

Bunin, B.A.; Ellman, J.A. J. Am. Chem. Soc. 1992, 114, 10997-10998.


Combinatorial Synthesis ofCombinatorial Synthesis of BenzodiazepinesBenzodiazepines

Bunin, B.A.; Ellman, J.A.J. Am. Chem. Soc. 1992, 114, 10997-10998.

TFA, H2O

Me2S

1)

2) R4X

1) pip

2) HOAc

R3

NFmoc F

H O

N O

Bn

OLi

R1

R2

N

OH

OR3

R1

R2

N

O

OR3

R2

N

O

O

OHN

OR3

R1O

NH

O

O

OHN

OR3

NH

Fmoc

R1

R2

O

NH2

O

O

OHN

R1

R2

N N

HN

R4R4


Combinatorial Synthesis ofCombinatorial Synthesis of BenzodiazepinesBenzodiazepines

Plunklett, M.J.; Ellman, J.A. J. Am. Chem. Soc. 1995, 117, 3306-3307.

Sieber, P.; Iselin, B. Helv. Chim. Acta 1968, 51, 622-632.

Pd2dba3.CHCl3, DIPEAK2CO3, THF, ArCOCl

O

O

OHN

NHBpoc

Ar

O

O

O

OHN

NHBpoc

SnMe3

NH2O

O

OONC

NHBpoc

SnMe3

Bpoc; stable to base, Stille cond'scleaved by very mild acid.

O O

O


SolubleSoluble BenzodiazepineBenzodiazepine LibraryLibrary

Cl Cl

N

NR4 O

R1

R2R3

R3

NHR4NH

R2ONH2.TFA

OR1 NR4NH

R2

OR1

O

+∆

TFA

Bunin, B.A.; Ellman, J.A. J. Am. Chem. Soc. 1992, 114, 10997-10998.


Safety CatchesSafety Catches

Kenner, G.W.; McDermott, J.R.; Sheppard, R.C. J. Chem. Soc., Chem. Commun. 1971, 636.

Marshall, D.L.; Liener, I.E. J. Org. Chem. 1970, 35, 807.

R',

polypeptide

1. MeI2. HO-

S NHMeO

O O

HN

R

R'HOS NHO

OO

HN

R

R'S NHO

OO

HN

R

Boc

H2O2 HO2CCH(R')NH2

O NHCbz

RNHHO2C

R'

CH2 S OHO

OCH2 S O

O NHCbz

RO

OCH2 S O

O NHCbz

R


CC--C Bond Formation: Safety CatchesC Bond Formation: Safety Catches

REAGENTS: i) LDA, THF, 0°C, then alkyl halide, 0 °C;ii) R-9-BBN or arylboronic acid, Pd(PPh3)4, Na2CO3, THF, 65 °C; iii) CH2N2, then HO-.

Backes, B.J.; Ellman, J.A. J. Am. Chem. Soc. 1994, 116, 11171-11172.

i

ii

iiiHO

O R'

RNH S N

OO

O

H

O R'

R

NH S N

OO

O

H

O Br

RNH S N

OO

O

H

O Br


Combinatorial Approach to Secondary StructureCombinatorial Approach to Secondary StructureMimeticsMimetics

Type I ββββ-turn

Somatostatin agonistNicolaou, Hirschmann, Smith III et al. Peptides 1989, 881-884. J. Am. Chem. Soc. 1992, 114, 9217-9218.

Hirschmann, Smith, III et al J. Am. Chem. Soc. 1992, 114, 9699-9701. Tetrahedron 1993, 49, 3665-3676.

CO2H

NH

NH2

NH

N

O HN

NH

H

O CO2H

O

NH

NH2

NH

NNH

O N

HO

O

Me

HN

O

N

NH2

O HN

O O H

H

O

O

OO

R

O

NH2

HN

HN


ββββββββ--Turn Mimic on Solid SupportTurn Mimic on Solid Support

BackboneNHNHO

Ri+2 NH

ORi+1

ORiRi+3

H2NO

NO

Ri+2 NH

ORi+1

S

Virgilio, A.A.; Ellman, J.A: J. Am. Chem. Soc. 1994, 116, 11580-11581.


ββββββββ--Turn Mimic on Solid SupportTurn Mimic on Solid Support

Virgilio, A.A.; Ellman, J.A: J. Am. Chem. Soc. 1994, 116, 11580-11581.

REAGENTS: i) α-Br-acid, DIC;ii) t-BuSS(CH2)nNH2; iii) Fmoc-amino acid, HATU; iv) piperidine,DMF; v) symmetric anhydride ofbromo acid; vi) Bu3P, H2O;vii) tetramethylguanidine;viii) 1:1:18 H2O/Me2S/TFA.

( )n

( )n

( )n( )n

i ii

iii

iv,v

vi

vii,vii

P = S-t-BuP = H

NHPh-NO2

HN

O

O

N SO

Ri+2 NH

ORi+1

NHPh-NO2

HN

O

O

N SPO

Ri+2 NH Br

ORi+1

NHPh-NO2

HN

O

O

HN SS-t-Bu

NHPh-NO2

HN

O

O

N SS-t-BuO

Ri+2NHFmoc

NHPh-NO2

HN

O

O

Br

NHPh-NO2

H2N

O


AnalysisAnalysis

! Monitor conversion on bead (e.g. Kaiser test for free primary amines)

! Analysis of reaction products on bead! Analysis of combinatorial mixtures of

products


IR on BeadIR on Bead

! 1971: resin beads of chloromethyl polystyrene oxidation products in KBr disks (Frechet J.M. J. Am. Chem. Soc. 1971, 93, 492-496.)

! FT-IR microspectroscopy: single bead from rxn to IR microscopy (Yan, R. J. Org. Chem.1995, 60, 5736-5738.

! Down to < 100 pmoles of material


IR on BeadIR on Bead

! FT-IR can monitor progress of reactions:

! Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS): fast, no sample preparation (Chan, T.Y. Tetrahedron Lett.1997, 38, 2821-2824).

OH O

OCOCl4

O

O

4N

O


NMRNMR

! C-13: low abundance, usually large sample quantities, long pulsing

! F-19, P-31 used also! MAS: nanoprobes allow for 10 mg resin

(Sarkar, S.K. J. Am. Chem. Soc. 1996, 118, 2305-2306.)


Mass spectrometryMass spectrometry

! MALDI-TOF MS: femtomole samples (Zambias, 1994,

! TOF-SIMS (Brummel, C.L. Science 1994, 264, 399-402)

! CE-ESI MS (Dunayevskiy, Y.M. Proc. Natl. Acad. Sci. 1996, 93, 6152-6157)


Is it feasible to make all possible interesting Is it feasible to make all possible interesting moleculesmolecules combinatoriallycombinatorially??

Mr500

•Only C,H,N,O

•Avogadro’s number

•Only one molecule each

• total mass: 10173 tonnes

•weight of Earth: 6.1021 tonnes!

•Weight of the Universe: ca 1084

tonnes!!!


ChallengesChallenges inin Combinatorial ChemistryCombinatorial Chemistry

• Development of diversity as a concept

• Development of solid phase synthesis

• Development of fast, chemoselective, high yield solution synthesis methods

• Development of high speed analysis

! Development of efficient screening strategies for minute amounts of compounds in mixtures


More SourcesMore SourcesReviews:! Dolle, R.E.; Kingsley, N.K. J. Combin. Chem. 1999, 1, 235-282.! Terrett, N.K. Combinatorial Chemistry OUP 1998, 186 pp.! Thompson & Ellman Chem. Rev. 1996, 96, 555-600.! Fruchtel & Jung Angew. Chem., Int. Ed. Engl. 1996, 35, 17-42.

! Asymmetric Catalysts:! Liu & Ellman J. Org. Chem. 1995, 60, 7712-7713.

! Web:! Tetrahedron Information System

! Molecular Diversity: Diversity Lovers’ Forum; http://vesta.pd.com/


Chemical Strategies in Drug DiscoveryChemical Strategies in Drug Discovery

Isolation

Structure BasedSynthesis

Rational Drug Design

Chemical Diversity Based Strategy

N

S

O

HN

CO2H

RCO

NH

N

NH

CN

S N

HN

N

NO

Cl

Tagamet(anti-ulcer)

Valium(tranquilizer)

ββββ-Lactams(antibiotics)

ONMe

HO

HO

N

N

O OH

H

H

H O

O

Progesterone

NOH

NOMe

Morphine Strychnine Quinine


Chemical Diversity Based StrategyChemical Diversity Based StrategyO

NH

O O

Me

Me

O

N

O O

Me

MeO

NH

O O

Me

MeBr O

OOO

Me

OBr

Me

split


Documents

1 out of 4000 candidates becomes a drug - UEF...1 out of 4000 candidates becomes a drug IND NDA 0 712years probability Drug Discovery Drug Development 11 March 2003 Ari Koskinen Note: