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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)