Gerhard Ecker Lecture 2

Pharmacoinformatic Approaches to target polyspecific Proteins Safety Sciences on the Molecular Level

Gerhard F. Ecker Emerging Field Pharmacoinformatics Department of Medicinal Chemistry, University of Vienna Althanstrasse 14, A-1090 Wien, Austria [email protected]; http://homepage.univie.ac.at/gerhard.f.ecker

G. Ecker

Pharmacoinformatics Target identification

Computational genomics

Target validation

Virtual screening

Computational systems biology

Identification & obtention of compounds

Structure-based drug design

Preclinical

Clinical

assessment

trials

ADMET prediction

Postmarketing monitoring

Medical Informatics

Biosimulation

Based on the molecular structure

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Drug Development - Failures

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Paradigm Shifts • One drug – one target • One drug – multiple targets (kinases)

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Paradigm Shifts • Many drugs – one target (hERG channel)

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Paradigm Shifts • Many drugs – many targets (ABC-transporter)

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Chemogenomics

H. Kubinyi, Vienna 2006 G. Ecker

Mapping the Chemical Space onto the Biological Space • Calculate pair wise similarity of all compounds active on a given target • Compare the average values with the “background” of the whole drug like chemical space • Requires approx. 20 mio x 20 mio similarity calculations G. Ecker

The Systems Biology View • ABC-transporter and Cytochromes are regulated by nuclear receptors • ABC-transporter and CYPs show overlapping substrate specificity • Selectivity has to be addressed on a systems level rather than on individual targets

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A Network of Targets

Ekins S, unpublished

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The ABC of Drug Transport • • • •

membrane-bound efflux pumps energy driven (ATP) ATP Binding Cassette (ABC-transporter) 48 ABC transporter in humans

– P-glycoprotein (P-gp, ABCB1) – Multidrug Resistance Related Protein (MRP, ABCC1) – Breast Cancer Resistance Protein (BCRP, MXR, ABCG2) • a lot of analogous transport proteins in bacteria, fungi, protozoes and plants very often multispecific in ligand recognition G. Ecker

P-Glycoprotein • • • • • • • •

170 kD 2 transmembrane domains 2 ATP-binding sites Xenotoxin transporter hydrophobic vacuum cleaner intestine, liver, kidney blood-brain barrier tumors G. Ecker

Substrates of P-Glycoprotein I Vinca Alkaloides Vincristine Vinblastine

Anthracyclines Doxorubicine Daunorubicine

Epipodophyllotoxines Etoposid Teniposid

Taxanes Actinomycin D

C.R. Leveille-Webster, I.M. Arias, J. Membrane Biol. 143, 89-102 (1995) G. Ecker

Inhibitors of P-Glykoprotein • Calcium Antagonists – Verapamil – Niguldipin

• Protein Kinase C Inhib. – Calphostin C – Staurosporin

• Calmodulin-Antagonists – Fluphenazin – Trifluoperazin – trans-Flupenthixol

• Cyclic Peptides – – – –

Cyclosporin A Valspodar FK 506 Rapamycin

• Miscellanous – – – –

Dipyridamol Quinidin Amiodaron Reserpin G. Ecker

Physiological Function of P-Glycoprotein • protection from toxins – blood brain barrier – testis – placenta

• excretion of toxins – liver – gastrointestinal tract – kidney Levin, J. Med. Chem. 23, 682 (1980) G. Ecker

Bioavailability and Transporter

Kim, Mol Pharm, 3, 26 (2006)

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Multispecificity - Challenges • Structure and function on the molecular level – – – –

kinetic studies photoaffinity labeling site specific mutagenesis protein homology modeling

• Design of inhibitors – promiscuity

• ADMET profiling – substrate yes/no? G. Ecker

Activity of Benzofurane-Analogs OH NR

O O

log(1/EC50)

R1

O

OH NR

R1

log(1/EC50) = 0.86 logP - 1.16 IBf - 3.33 (Q2cv = 0.97)

logP ber. J. Csöllei, J. Med. Chem. 39, 4767-4774 (1996) G. Ecker

P-Glycoprotein - the Target Optimal distance: 3.5 -CH2-

π−π-interaction

high partial logP

OH N

O

steric interactions

O

H-bond acceptor

H-bond acceptor

• Hansch-Analysis • Free-Wilson Analysis • Topliss-Approach

π−π-interaction

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Pharmacophoric Features 15 diverse compounds multiconformational-DB Mapping of the features: hydrophobic aromatic H-bond acceptor positive ionizable

Chemical function based pharmacophoric features - CATALYST Langer, Arch. Pharm. 337, 317 G. Ecker

Screen of the World Drug Index F

NO2

HO

HO O

OH N

O

N

O

O

F

N H

Terfenadine

Benidipine

AHR-16303B

O

OH N

O OH

N

O

HO N

N

N

O

O

HO

N

H N

N

N

CGP-54103

CP-215548

CP-117227

N N

OH

O

N

HN N

N

CF3

O

HO S

O

Asocainol

Homofenazine

Cl

N

Mepacrine

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Virtual Screen of the SPECS Compound Library • increase network size to 250 x 250 • projection of the propafenons together with the SPECS database (134.767 compounds) • analyse co-localisations

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Kohonen Maps - Hits O

O

N

N

O

N

N

N

N

O

N

O

N N N

N N

S

AG-690/11972772

N

O

AG-690/12887361

S

Cl

AJ-131/15197008

NH2

AJ-292/13162028

O

N

O

N

O

S

N N

S

N

N O

N

S

S N

AJ-292/15089034

AN-989/14669159

AO-364/14480185

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Benzophenones as tool for characterisation of the “Propafenon-Site” on P-glycoprotein z z

z z

high activation wavelength (>340nm) short half life (10-13 sec) in presence of C-H groups repeated activation cycles possible photoactivation takes place on a pharmacophoric sub-structure

OH NR

O O

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Consensus-labeling Regions

Ecker, Mol. Pharmacol. 61, 637 (2002) G. Ecker

Extension to P-glycoprotein

Pleban, Mol Pharmacol 67, 365 (2005)

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Selectivity Profiling B1/C1/G2 • ABCB1, ABCC1 and ABCG2 have different physiological functions and tissue distribution • in part overlapping substrate specificity • Polyspecific inhibitors might have advantages in tumor therapy • Selective inhibitors might overcome side effects due to physiological functions • Problem of promiscuity! G. Ecker

Selectivity Profiling B1/G2

ABCB1

ABCG2 G. Ecker

Selectivity Profiling ABCB1 vs. ABCG2 2

1 log potency ABCG2 (R482R)

• ABCG2 (MXR, BCRP) is responsible for resistance to methotrexate in breast cancer • propafenones inhibit both pumps • selectivity up to 1000 fold • main difference: H-bond acceptor strenght in the vicinity of the nitrogen-atom

0

-1

-2

-3 -3

-2

-1

0

1

log potency ABCB1

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2

Selectivity Profiling B1/G2

ABCB1

ABCG2

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Computational Sciences

LEWI-GRID Docking MD-Simulations Binding free energy

Faculty of Informatics

CPAMMS

Emerging Field Pharmacoinformatics

Joint Publications/Projects C.R.Noe: BBB,NMDA,Polyamines T.Erker: COX W.Holzer: P-gp W.Jäger: CYP S.Hering: hERG channel

Computational Life Sciences

PiP-Vie Compunds Properties Reverse Screening

MUW Barcelona Perugia Erlangen

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EUROPIN – A European Pharmacoinformatics Initiative EUROPIN brings together six institutions from five European Countries to develop a joint PhD program on Pharmacoinformatics in order to promote training and education of top level scientists in this field. It will provide a platform for training through research focusing on methods and applications used in computational drug design and development. University of Vienna (coordinator) Pompeu Fabra University, Barcelona Gdansk University of Technology Martin-Luther-University Halle-Wittenberg University of Parma University of Perugia G. Ecker

EUROPIN - Objective Core objectives are • to promote creativity, competitiveness, employability and entrepreneurial spirit of young scientists.

These will be achieved • via strong emphasis on cooperation and mobility of students and teaching staff, • by use of intensive programmes and workshops with strong participation of experts from Pharmaceutical Companies, • and by extensive use of web-based virtual training activities.

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Thank you! Dominik Kaiser Barbara Zdrazil Karin Pleban Michael Demel Rita Schwaha Khac-Minh Thai Lars Richter Andrea Schiesaro Daniela Digles Yogesh Aher

Wilfried Gansterer Peter Chiba Michael Gottesman Roberto Pellicciari Ferran Sanz Johnny Gasteiger

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