COMBINATORIAL CHEMISTRY OF SMALL ORGANIC...

Angel Messeguer

IQAC (CSIC)Barcelona

COMBINATORIAL CHEMISTRY

OF SMALL ORGANIC MOLECULES

X

XC C CC

Scope

Introduction

Combinatorial libraries and drug discovery

Libraries of controlled mixtures of peptoids

Neuroprotection

Modulation of protein-protein interactions

Business opportunities

Scope

Introduction

Combinatorial libraries and drug discovery

Libraries of controlled mixtures of peptoids

Neuroprotection

Modulation of protein-protein interactions

Business opportunities

COMBINATORIAL CHEMISTRY

METHODS FOR THE MULTIPLE SIMULTANEOUS OR PARALLEL

SYNTHESIS OF A SIGNIFICANT NUMBER OF COMPOUNDS WITH

WELL DEFINED LEVELS OF DIVERSITY.

X

XC C CC

COMBI

CHEMLIBRARIES

DIVERSITY

COMBINATORIAL CHEMISTRY LEVELS

Combinatorial strategies

Amino acids andnucleic acids as building blocks

LIFENATURE

IMMUNESYSTEM

Combinatorial production of antibodies

Production of specificantibodies after recognition

Peptide andoligonucleotide libraries

Libraries of small

organic molecules

Catalysts and materials

ORGANIC CHEMISTRY

INORGANIC CHEMISTRY

COMBINATORIAL

CHEMISTRY

COMBINATORIAL CHEMISTRY AND ORGANIC CHEMISTRY

POTENTIAL FOR NEW DISCOVERIES (Bohacek et al., 1996)

Stable structures from 30 elements: C, O, N, S, H 1063

With 1 mg available 1060

g

Mass of the sun 2 x 1033

g

Mass of the universe 1063

g

The organic library 1027

sunsNot enough suns

Not enough carbon

Current chemical universe: 50 million compounds.

1 mg available represent 50 Kg

(or the ratio of the mass of one proton to the mass of the sun)

NEGLIGIBLE SMALL COMPARED TO THE POSSIBLE DIVERSITY

HISTORY:

1984 Parallel synthesis or "pines" Geysen

Late 80s Combinatorial concept (Furka)

Early 90s Methods development, peptide synthesis, solid phase

92 Entry of major pharmaceutical companies

95 World wide interest

2000 4 Publications per day

over 1 billion dollars in business

COMBINATORIAL CHEMISTRY

CatalysisMaterials Science

AgronomicsMedicinalChemistry

COMBINATORIAL CHEMISTRY LIBRARIES

Electrochemistry HPLC Chiral Ligands

COMBINATORIAL

CHEMISTRY

Use of high advanced concepts of ORGANIC SYNTHESIS

Well-definedbuilding blocks

Synthetic strategies

LIBRARIES OF ANY KIND

LIMITATION INDRUG DEVELOPMENT

Access to structural diversitywithin the limits of known chemistry

COMBINATORIAL CHEMISTRY AND MEDICINAL CHEMISTRY

2-4 years DISCOVERY 10.000 compounds

7-12 DEVELOPMENT 10

9-16 MARKETED DRUG 1

600-800 MILLION EUROSCOST AND TIME MINIMISATION

THE DRUG DISCOVERY ADVENTURE

TARGET IDENTIFICATION

LEAD IDENTIFICATION

LEAD OPTIMISATION

*

*

*

BOTTLENECKS

EARLY PHASES

Owens Nature Reviews Drug Discovery 6, 99–101 (February 2007) | doi:10.1038/nrd2247

FDA APPROVED NEW MOLECULAR ENTITIES

THE DRUG DISCOVERY ADVENTURE

THE DRUG DISCOVERY ADVENTURE

Kennedy, S.P., Bormann, P.J., Exp. Biol. Med. 2006, 231, 1690

THE DRUG DISCOVERY ADVENTURE

Kennedy, S.P., Bormann, P.J., Exp. Biol. Med. 2006, 231, 1690

THE DRUG HUNTING PROCESS

Target Selection Lead Identification Lead Optimization

Identification of

potential targets

Target verification

Target selection

Target validation

Screen development

High-throughput

screening

Secondary assays /

Mechanism of action

Hits Leads

Lead optimization

Potency in disease

Pharmacokinetics

Early toxicology

Drug Candidates

Biological Assays

Rational Drug Design

Recombinant Proteins

Existing Individual Collections

TraditionalChemical Synthesis SAR

PotentialTherapeutical Compounds

HISTORICAL APPROACHES TO DRUG DISCOVERY

Existing Individual CollectionsExisting Individual Collections

Chemical Synthesis SAR

Ferment & Find

(Bacterial Broth)

Grind & Find

(Natural Sources)

Biological Assays

Rational Drug Design

Recombinant Proteins

Existing Individual Collections

TraditionalChemical Synthesis SAR

Combinatorial Libraries

PotentialTherapeutical Compounds

HISTORICAL APPROACHES TO DRUG DISCOVERY

Existing Individual Collections

TraditionalChemical Synthesis SAR

Existing Individual Collections

Chemical Synthesis SAR

Ferment & Find

(Bacterial Broth)

Grind & Find

(Natural Sources)

Scope

Introduction

Combinatorial libraries and drug discovery

Libraries of controlled mixtures of peptoids

Neuroprotection

Modulation of protein-protein interactions

Business opportunities

GENOMICS

DRUG

DISCOVERY

PROTEOMICS

BIOINFORMATICS

HIGH THROUGHPUT SCREENING

COMBINATORIAL CHEMISTRY

THE DRUG DISCOVERY IN THE NEW CENTURY

COMBINATORIAL CHEMISTRY AND DRUG DISCOVERY

R1

R2

R3

Target structural

requirements

THERAPEUTIC

TARGET

COMBINATORIAL CHEMISTRY AND DRUG DISCOVERY

VIRTUAL LIBRARY

PR

EC

LIN

ICA

L P

ER

IOD

R1

R2

R3

Target structural

requirements

THERAPEUTIC

TARGET

COMBINATORIAL CHEMISTRY AND DRUG DISCOVERY

VIRTUAL LIBRARY

DIVERSITY

FILTRATION

FOCUSED

LIBRARY

PR

EC

LIN

ICA

L P

ER

IOD

Pharmacodynamic

Pharmacokinetic

Pharmaceutic

R1

R2

R3

Target structural

requirements

THERAPEUTIC

TARGET

Individuals

Restrictions:

COMBINATORIAL CHEMISTRY AND DRUG DISCOVERY

VIRTUAL LIBRARY

DIVERSITY

FILTRATION

FOCUSED

LIBRARY

HITS

Activity assays

(HTS)

PR

EC

LIN

ICA

L P

ER

IOD

Pharmacodynamic

Pharmacokinetic

Pharmaceutic

R1

R2

R3

Target structural

requirements

THERAPEUTIC

TARGET

Individuals

Restrictions:

LEADS

Optimisation

(Combichem)

COMBINATORIAL CHEMISTRY AND DRUG DISCOVERY

1992-2005:

OVER 60 COMPOUNDS IN HUMAN TRIALS FROM HIGH

THROUGHPUT SCREENING OF LIBRARIES

S

Cl

SN

O O

N

N

O

H

Antagonist of 5-HT6 receptor

H

N

H

NN

N

N

O

N

N

H

NN

N

N

N

H

O

CF3

N

N

STI571 (Gleevec)

AMN107 (Tasigna)

COMBINATORIAL CHEMISTRY OF SMALL ORGANIC MOLECULES

INDIVIDUAL COMPOUNDS

- Spatially addressed chemical synthesis

- Multiple parallel organic synthesis

CONTROLLED MIXTURES

- Split and mix

- Positional scanning

LIBRARY FORMATS

Libraries of discretes

Easy development of library chemistry

Automatisation of synthesisDirect individual screening for biological activity

Demands high capacity of screening

Only small libraries made by hand

Optimize leads

Focused libraries

Increasingly preferred by companies

COMBINATORIAL CHEMISTRY OF SMALL ORGANIC MOLECULES

LIBRARY FORMATS: PROS AND CONS

LIBRARY FORMATS: Positional Scanning

Rm = random mixture

1 2 3

A

Rm 2

Rm 3

ALSALTALUAMSAMTAMUANSANTANU

B

Rm 2

Rm 3

BLSBLTBLUBMSBMTBMUBNSBNTBNU

C

Rm 2

Rm 3

CLSCLTCLUCMSCM

CMUCNSCNTCNU

3 x 3 x 3 = 27 compounds

T

LIBRARY FORMATS: Positional Scanning

Rm = random mixture

1 2 3

A

Rm 2

Rm 3

ALSALTALUAMSAMTAMUANSANTANU

B

Rm 2

Rm 3

BLSBLTBLUBMSBMTBMUBNSBNTBNU

C

Rm 2

Rm 3

CLSCLTCLUCMSCM

CMUCNSCNTCNU

Kn Rm Rm

OXX

3 x 3 x 3 = 27 compounds

T

LIBRARY FORMATS: Positional Scanning

Rm = random mixture

1 2 3 4 5 6

A

Rm 2

Rm 3

ALSALTALUAMSAMTAMUANSANTANU

B

Rm 2

Rm 3

BLSBLTBLUBMSBMTBMUBNSBNTBNU

C

Rm 2

Rm 3

CLSCLTCLUCMSCM

CMUCNSCNTCNU

Rm 1

L

Rm 3

ALSBLSCLSALTBLTCLTALUBLUCLU

Rm 1

N

Rm 3

ANSBNSCNSANTBNTCNTANUBNUCNU

Rm 1

M

Rm 3

AMSBMSCMSAMTBMTCMTAMUBMUCMU

Kn Rm Rm

OXX

Rm Kn Rm

XOX

3 x 3 x 3 = 27 compounds

T

LIBRARY FORMATS: Positional Scanning

Rm = random mixture

1 2 3 4 5 6 7 8 9

A

Rm 2

Rm 3

ALSALTALUAMSAMTAMUANSANTANU

B

Rm 2

Rm 3

BLSBLTBLUBMSBMTBMUBNSBNTBNU

C

Rm 2

Rm 3

CLSCLTCLUCMSCM

CMUCNSCNTCNU

Rm 1

L

Rm 3

ALSBLSCLSALTBLTCLTALUBLUCLU

Rm 1

N

Rm 3

ANSBNSCNSANTBNTCNTANUBNUCNU

Rm 1

Rm 2

S

ALSBLSCLSAMSBMSCMSANSBNSCNS

Rm 1

Rm 2

T

ALT

BLTCLTAMTBMTCMTANTBNTCNT

Rm 1

Rm 2

U

ALUBLUCLUAMUBMUCMUANUBNUCNU

Rm 1

M

Rm 3

AMSBMSCMSAMTBMTCMTAMUBMUCMU

Kn Rm Rm

OXX

Rm Kn Rm

XOX

Rm Rm Kn

XXO

3 x 3 x 3 = 27 compounds

T

LIBRARY FORMATS: Positional Scanning

Rm = random mixture

- 3 Libraries with different structure of mixtures- Easy automatisation- Direct deconvolution

1 2 3 4 5 6 7 8 9

A

Rm 2

Rm 3

ALSALTALUAMSAMTAMUANSANTANU

- Library chemistry (relative kinetics)

B

Rm 2

Rm 3

BLSBLTBLUBMSBMTBMUBNSBNTBNU

C

Rm 2

Rm 3

CLSCLTCLUCMSCM

CMUCNSCNTCNU

Rm 1

L

Rm 3

ALSBLSCLSALTBLTCLTALUBLUCLU

Rm 1

N

Rm 3

ANSBNSCNSANTBNTCNTANUBNUCNU

Rm 1

Rm 2

S

ALSBLSCLSAMSBMSCMSANSBNSCNS

Rm 1

Rm 2

T

ALT

BLTCLTAMTBMTCMTANTBNTCNT

Rm 1

Rm 2

U

ALUBLUCLUAMUBMUCMUANUBNUCNU

Rm 1

M

Rm 3

AMSBMSCMSAMTBMTCMTAMUBMUCMU

Kn Rm Rm

OXX

Rm Kn Rm

XOX

Rm Rm Kn

XXO

3 x 3 x 3 = 27 compounds

T

POSITIONAL SCANNING

NL M S UT

!!

A CB

!

diversity element

defined position

aleatory position

! =

=

=

COMBINATORIAL LIBRARIES

Deconvolution:

XXOOXX XOX

! !

B, C

L, N

T

Synthesis of:

B-L-T

B-N-T

C-L-T

C-N-T

LIBRARY FORMATS: PROS AND CONS

Positional scanning:

- Easy synthesis automatisation- Direct deconvolution with several possible hits - Low number of biological assays required

- Biological testing of mixtures (non independent activities)- Complex development of library chemistry (relative kinetics)

- Random screening for new leads

DYNAMIC COMBINATORIAL LIBRARIES

Dynamic library: set of molecules resulting from the reversible

formation of covalent bonds or molecular interactions .

Deconvolution: The interaction with the target shifts the equilibrium

thus making possible the identification of the active components

A1-i B1-j+ A1-i B1-j

Virtual library

Components Available

diversity

Imine formation

Aldol formation

Disulfide formation

Metal coordination

Cis-trans isomerisation

Tautomerism

J.M. Lehn, Chem. Eur. J. 1999

O + H2N R NR

H

O

H

O+

OH O

SHHS+ S S

Mm+ nL+ [MLn]m+

X XX X

NH

O N OH

DYNAMIC COMBINATORIAL LIBRARIES

THE CHEMICAL GENETICS CONCEPT

S. Schreiber

(Harvard)

Scope

Introduction

Combinatorial libraries and drug discovery

Libraries of controlled mixtures of peptoids

Neuroprotection

Modulation of protein-protein interactions

Business opportunities

Libraries of controlled mixtures of peptoids

PEPTIDE

PEPTOIDS: Oligomers of N-Alkylglycines

NO

N

O

N

O

N

O R3

R2

R1

H

H

H

PEPTOIDPROS:

! Metabolic stability

! Wide chemical diversity

! Less steric restrictions2

NO

N

RO

N

O

N

R1R3

O

Libraries of controlled mixtures of peptoids

2

NH

O

N

RO

N

O

NH2

R3

R1

PEPTOID

Great conformational mobility

PROS CONS

More than one active

conformation

(undesired side effects)

Wide optimisation range

(opposite to a rigid hit)

HIT TO LEAD

Libraries of controlled mixtures of peptoids

" Format: positional scanning

" Number of compounds : 20 x 16 x 16 = 5.120

" Solid phase synthesis

52 controlled mixtures

16 ( X X O )

16 ( X O X )

20 ( O X X )

2

NH

O

N

RO

N

O

NH2

R3

R1

LIBRARY OF PEPTOIDS

M. Humet et al, J. Comb. Chem. 2003, I. Masip et al., Bioorg. Med. Chem., 2005)

Libraries of controlled mixtures of peptoids

" Biological screening

LIBRARY OF PEPTOIDS

PeptoidsCancer

MDR(JPET, 2005)

Serine proteases

NeuroprotectionJPET, 2002

??

AnalgesiaTRPV1

PNAS, 2002

AntibioticsJ. Comb. Chem., 2003

NMDA AntagonistsJPET, 2002

Neuronal

regeneration

Septic shock LPSJ. Med. Chem., 2005

Apoptosis APAF(Cell Death Differ, 2006)

Cancer

UBC13-UEV (2007)

Libraries of controlled mixtures of peptoids

" Biological screening

LIBRARY OF PEPTOIDS

PeptoidsCancer

MDR(JPET, 2005)

Serine proteases

Neuroprotection??

JPET, 2002

AnalgesiaTRPV1

PNAS, 2002

AntibioticsJ. Comb. Chem., 2003

NMDA AntagonistsJPET, 2002

Neuronal

regeneration

Septic shock LPSJ. Med. Chem., 2005

Apoptosis APAF(Cell Death Differ, 2006)

Cancer

UBC13-UEV (2007)

(In preparation)

Semaphorins

January, 2009

Libraries of controlled mixtures of peptoids

AnalgesiaTRPV1 antagonists

PNAS, 2002, 99, 2374

PEPTOIDS IDENTIFIED EXHIBITING

IN VITRO AND IN VIVO ACTIVITIES

NHN

N

O

NH2

O

O

N16-15-15C

MW 643

N19-15-15C

MW 645

NNHN

N

O

NH2

O

O

N

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Unknown topology of the receptor and of its interaction with these antagonists

Use of conformationally restricted analogues of these peptoids for

reducing undesired side-effects

obtaining structural information about TRPV1 target

Libraries of controlled mixtures of peptoids

Neuroprotection

JPET, 2002, 301, 29

JPET, 2002, 302, 163

PEPTOIDS IDENTIFIED EXHIBITING

IN VITRO AND IN VIVO ACTIVITIES

NNH

NN

O

NH2

O

O

N6-1-2C N6-1-10C

NNH

NN

O

NH2

O

O

Target unknown

Use of conformationally restricted analogues of these peptoids for

obtaining structural information about the target

Use of peptoids attached to polymer supports (Sepharose) for capturing

potential targets

Scope

Introduction

Combinatorial libraries and drug discovery

Libraries of controlled mixtures of peptoids

Neuroprotection

Modulation of protein-protein interactions

Business opportunities

Development of new inhibitors of polyubiquitylation through

disruption of the UBC13-UEV1 complex.

UBC13UBC13

UBC13-UEV complex is responsible

of the formation of non-canonical

(Lys63) polyubiquitin chains.

PUq chains modify substrate proteins

that participate in signaling pathways,activation of NF-"B, and other

essential cell cycle regulation

processes.

UBC13-UEV regulates processes that

generally enhance the survival of cells

in response to certain forms of stress.

Modulation of UBC13-UEV1 interaction

Modulation of UBC13-UEV1 interaction

Yeast two-hybrid assay Yeast two-hybrid assay as a as a screen tool to identify smallscreen tool to identify small

molecule protein-protein interaction antagonistsmolecule protein-protein interaction antagonists

Gal4Gal4

DBDDBD

UBC13UBC13

promoter HIS3 ADE2 lacZ

ADAD

UEV1UEV1Growth #-gal activity

NO NO (LOW)

Gal4Gal4

DBDDBD

UBC13UBC13

promoter HIS3 ADE2 lacZ

ADAD

UEV1UEV1

XX

NO NO (LOW)

Gal4Gal4

DBDDBD

UBC13UBC13

promoter HIS3 ADE2 lacZ

ADADUEV1UEV1

YES YES (HIGH)

transcription

LIBRARY OF PEPTOIDS (5.120)

IDENTIFICATION OF 4 ACTIVE COMPOUNDS

Screening

COMPUTATIONAL STUDIES: DOCKING OF

CONFORMATIONALLY RESTRICTED ANALOGUES

LEAD CANDIDATES

Synthesis and biological evaluation

Modulation of UBC13-UEV1 interaction

Library deconvolution: identification of hits

HN

O

O

NNH2

O

N

F

F

HN

O

O

NNH2

O

N

Cl

F

Cl

HN

O

O

NNH2

O

F

F

HN

O

O

NNH2

O

Cl

F

Cl

O

O

N37-37-9C N37-37-13C

N15-37-13CN15-37-9C

Modulation of UBC13-UEV1 interaction

Design of conformationally restricted analogs through docking

analysis (CDOCK) againsts UBC13

Ia IIa

Best compounds determined by virtual screening: both from peptoid N37-37-9C

Scheper, J. et al, submitted for publication

Modulation of UBC13-UEV1 interaction

Scope

Introduction

Combinatorial libraries and drug discovery

Libraries of controlled mixtures of peptoids

Neuroprotection

Modulation of protein-protein interactions

Business opportunities

Scientific and technologic research has grown significantly in

recent years

PUBLICATIONS:

Quantity 0.97% in 1981-85 to 2.37% in 1993-1997

Quality Impact factor multiplied per 2.2 within the

1981-1997 period

THS INCREASE IS THE RESULT OF THE INVESTMENT IN

INFRASTRUCTURE AND PERSONNEL TRAINING.

Technology Transfer: from Academy to Business

SCIENTIFIC AND TECHNOLOGIC RESEARCH IN CHEMISTRY

AND LIFE SCIENCES

HIGH LEVEL SCIENTISTS

(risks of specialisation in poor market areas)

EXCESS OF TECHNOLOGY AND KNOWLEDGE

(Academy is not ready to absorb this excess)

ACADEMIA: UNIVERSITIES, SCIENCE PARKS, CSIC

Technology Transfer: from Academy to Business

ACADEMIA COMPANY

TRANSFER OF TECHNOLOGY OR KNOWLEDGE

CONTRACTS BETWEEN COMPANIES AND INSTITUTIONS

CONTRACTS BETWEEN SCIENTISTS AND COMPANIES

Technology Transfer: from Academy to Business

ACADEMIA COMPANY

INSTITUTE

SPIN-OFF

OTHER POSSIBILITIES

TRANSFER OF TECHNOLOGY OR KNOWLEDGE

Technology Transfer: from Academy to Business

CREATION OF A SPIN-OFF

IN BIOTECHNOLOGY OR IN THE PHARMACEUTICAL AREA

?

Technology Transfer: from Academy to Business

THE DRUG DISCOVERY ADVENTURE

2-4 years DISCOVERY 10.000 compounds

7-12 DEVELOPMENT 10

9-16 MARKETED DRUG 1

400-800 MILLION EUROCOST AND TIME MINIMISATION

TARGET IDENTIFICATION AND VALIDATION

HIT IDENTIFICATION ANDLEAD OPTIMISATION

BOTTLENECKS(EARLY PHASES)

OUTSOURCING

Technology Transfer: from Academy to Business

Preclinical trials:

Chemistry and synthesis

Efficacy in animals

Bioavailability

Pharmacokinetics

Toxicology

Clinical trials:

Phase 1

Phase 2

Phase 3

0 2 4 6 8 10 12

Years

Re

gis

ter

DRUG DEVELOPMENT PROCESS

BIG

PHARMA

SPIN-OFF A SMALL PIECE OF THE CAKE

Technology Transfer: from Academy to Business

?

CREATION OF A SPIN-OFF

IN BIOTECHNOLOGY OR IN THE PHARMACEUTICAL AREA

Technology Transfer: from Academy to Business

A TECHNOLOGY OR A PRODUCT INTERESTING TO MARKET

WELL DEFINED INTELLECTUAL PROPERTY

HUMAN CAPITAL

BUSINESS PLAN

INVESTORS

Initial requirements:

CREATION OF A SPIN-OFF

IN BIOTECHNOLOGY OR IN THE PHARMACEUTICAL AREA

Technology Transfer: from Academy to Business

A TECHNOLOGY OR A PRODUCT INTERESTING TO MARKET

SERVICES

RESEARCH AND DEVELOPMENT (INNOVATION)

PRODUCT

KNOW-HOW

Technology Transfer: from Academy to Business

WELL DEFINED INTELLECTUAL PROPERTY

INTELLECTUAL PROPERTY

PATENT OR PUBLISH PATENT AND PUBLISH

ROLE OF PUBLIC INSTITUTIONS

TRAINING OF SPECIALISED PERSONNEL

FACILITATING TECHNOLOGY TRANSFER

Technology Transfer: from Academy to Business

HUMAN CAPITAL

TRAINED SCIENTISTS (PhDs + postdoc periods)

TECHNICIANS

University degree

Technical degree

!

!

INCORPORATION OF UNIVERSITY OR PUBLIC CENTRES

STAFF

CEO, CSO AND CONSULTORS MARKET

?

?

Technology Transfer: from Academy to Business

BUSINESS PLAN INVESTORS

SUPPORT FROM PRIVATE COMPANIES OF THE AREA

SUPPORT PUBLIC INSTITUTIONS

BIOINCUBATORS

SUBVENTIONS

FINANCING

BUSINESS PLAN

CAPITAL RISK

SPAIN

EUROPE

Technology Transfer: from Academy to Business

PharmaMar

Lipotec

Crystax

Advancell

……..

DiverDrugs

Technology Transfer: from Academy to Business

Acknowledgements

Bioorganic Chemistry

Group (IQAC)

Jordi Bujons

Isabel Masip

Nuria Cortés

Sandra Moure

Gloria Sanclimens

Marisa Guardiola

Marc Huguet

Joaquim Messeguer

Miquel Vidal

Glòria Vendrell

Miriam Corredor Economic support

Ministry for Science and Innovation

Fundació Marató TV3

PETRI Projects

EU Projects (FEDER)

DiverDrugs, S.L.

Collaborations

Enrique Pérez-Payá (FVIB, Valencia)

Gema Malet

Antonio Ferrer-Montiel (UMH, Elche)

María José Abad

José Ferragut (UMH, Elche)

Vicente Felipo (FVIB, Valencia)

Carmina Montoliu

Timothy Thomson (IBMB, Barcelona)

Johanna Schepper (IBMB, Barcelona)