Development of methods for the analysis of ligand-protein

interactions by

Maris Lapinsh; Advisor Jarl Wikberg Division of Pharmacology, Uppsala University

©Maris Lapinsh 2002

- Lapinsh et al. (2001) Development of proteo-chemometrics: a novel technology for the analysis of drug-receptor interactions. Biochim. Biophys. Acta, 1525(1).

- Lapinsh et al. (2002) Proteo-chemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands, Mol. Pharm., 61(6).

- Lapinsh et al. (2002) Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences, Protein Sci., 11(4).

©Maris Lapinsh 2002

multiple linear regression,

partial least-squares projections to latent structures,

neural networks etc.

- which ligand properties that are importantfor the recognition of the target protein- how to increase ligands affinity for the target

- is any of the ligands selective for the given target- which ligand AND protein properties determine selectivity- how to improve selectivity for the target

©Maris Lapinsh 2002

- which ligand properties that are importantfor the recognition of the target protein- how to increase ligands affinity for the target

- is any of the ligands selective for the given target- which ligand AND protein properties determine selectivity- how to improve selectivity for the target

©Maris Lapinsh 2002

Interaction data

Lapinsh et al., Mol.Pharm., 2002.

D1

D2

D3

D4

5HT

1A5H

T1B

5HT

1D5H

T1E

5HT

1F5H

T2A

5HT

2B5H

T2C

5HT

65H

T7

1A 2A 2B 2C 1 2 H1

ORG5222 8.8 8.8 8.8 8.7 8.2 8.4 8.1 8.0 9.8 9.8 9.6 9.0 9.1 9.2 8.2 9.3 7.9 5.3 5.3 9.8

Zotepine 8.1 8.2 7.4 6.5 7.3 7.2 6.5 8.6 6.7 8.2 6.8 5.4 5.6 9.2

Fluparoxan <6 <6 6.8 <6 <6 <6 <6 6.3 8.1 8.9 8.8 pKiOlanzapine 7.9 7.9 7.4 7.6 5.7 6.2 6.3 5.7 6.5 8.8 8.1 8.1 8.0 7.0 7.7 6.1 6.7 6.7 5.3 5.3 9.2 >9Clozapine 7.8 6.9 6.6 7.4 6.9 6.4 6.2 6.4 6.9 8.4 8.8 7.3 8.0 7.3 8.9 7.0 7.7 7.9 5.3 5.8 9.6 8 - 9S16924 7.5 7.3 8.0 8.7 9.0 8.4 7.7 7.6 7.1 8.7 6.8 7.4 7.0 5.0 5.7 7 - 8

S18327 7.2 7.1 7.0 8.1 7.4 8.5 6.4 9.0 7.0 6 - 7

Amperozide 6.7 6.3 6.4 5.6 <6 8.2 5.6 7.4 5.9 <6

GGR218231 <6 7.2 9.0 5.0 6.8 <6 <6 <6 <6 <6 <6 6.4

Sertindole 7.7 8.4 8.1 7.7 6.5 7.2 7.0 6.4 6.4 9.7 8.7 9.9 6.4 6.3 6.3 5.3 5.3 6.9

MDL100,907 6.6 <6 4.9 6.2 5.0 9.2 7.6 6.6 5.0

Haloperidol 8.5 9.1 8.3 8.4 5.8 6.6 5.3 5.3 5.3 6.9 <6 5.0 <6 6.6 8.2 5.9 6.2 5.9 5.3 5.3 6.1

Tiospirone 7.4 8.7 8.6 8.3 8.4 9.3 8.3 9.6 6.7

Raclopride 5.0 8.9 8.8 5.4 5.1 6.7 5.0 5.0 5.0

Fluspirilene 9.0 8.4 8.5 7.3 6.0 5.3 5.7 8.0 6.2 7.3 7.2 6.2 6.3 7.9

Ocaperidone 7.6 9.2 8.6 8.5 8.0 10.0 8.0 9.7 7.7

Risperidone 7.7 8.4 7.9 8.0 6.5 8.0 6.9 5.9 5.9 9.3 7.8 9.3 7.6 8.1 8.0 5.3 5.3 7.6

S33084 6.3 7.5 9.6 5.7 <6 6.1 6.9 6.0 6.8 7.1 6.9 <6

L741626 6.1 8.4 7.2 6.5 <6 <6 <6 6.5 6.2 <6 6.6 5.9

Seroquel 6.7 6.5 6.4 5.7 6.5 5.7 5.3 5.9 5.6 6.8 7.0 6.2 5.5 6.6 8.0 5.3 7.0 6.5 5.3 5.3 8.7

Yohimbine 6.4 5.4 7.3 6.8 7.6 <6 <6 6.7 8.3 8.7 9.6 <6 <6

Ziprasidone 8.5 8.3 8.0 7.6 8.4 9.0 8.3 6.4 9.2 8.4 8.7 7.6 8.2 8.9 6.6 7.3 7.1 5.6 5.3 7.8

Pipamperone 6.9 6.6 8.3 5.6 6.8 6.2 5.3 5.3 8.3 6.1 7.5 6.5 5.3 5.3 5.6

1

©Maris Lapinsh 2002

Molecular Interaction Fields

Description of organic compounds and amino acids

Bitstrings

2

©Maris Lapinsh 2002

Molecular Interaction Fields 5 Z-scalesBitstrings

Description of organic compounds and amino acids

2

©Maris Lapinsh 2002

5 Z-scales

Description of organic compounds and amino acids

2

©Maris Lapinsh 2002

Description of the whole protein sequences

alignment based alignment independent

- Lapinsh et al. Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences, Protein Sci., 2002.

3

©Maris Lapinsh 2002

- Lapinsh et al. Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences, Protein Sci., 2002.

External prediction of membership to GPCR class

0%

97%

©Maris Lapinsh 2002

Ligand-protein cross description4

©Maris Lapinsh 2002

D1

D2

D3

D4

5HT

1A5H

T1B

5HT

1D5H

T1E

5HT

1F5H

T2A

5HT

2B5H

T2C

5HT

65H

T7

1A 2A 2B 2C 1 2 H1

ORG5222ZotepineFluparoxanOlanzapine >9Clozapine 8 - 9S16924 7 - 8

S18327 6 - 7

Amperozide <6

GGR218231

Sertindole

MDL100,907

Haloperidol

Tiospirone

Raclopride

Fluspirilene

Ocaperidone

Risperidone

S33084

L741626

Seroquel

Yohimbine

Ziprasidone

Pipamperone

21 amine G-protein coupled receptors

23 organic amines

Application of proteo-chemometrics on amine GPCRs

Lapinsh et al., Mol.Pharm., 2002.©Maris Lapinsh 2002

Amine GPCRs Organic compounds

7 TM * 25 aa * 5 z-scales = 875

6 * 52 MIF descriptors =312

Lapinsh et al., Mol.Pharm., 2002.

-PCA?

-”One way” analysis for variable selection?

-Prior knowledge?

-PCA on descriptor blocks?

Ligand-receptor cross description

?

©Maris Lapinsh 2002

- Centering and scaling- Variable selection- Cross validation- Validation by responce permutations- External predictions

Partial least-squares projections to latent structures

©Maris Lapinsh 2002

Lapinsh et al, Mol.Pharm., 2002.

Output of PLS modelling:

5

6

7

8

9

10

5 6 7 8 9 10

Observed pKi

Cal

cula

ted

/pre

dic

ted

pK i

Calculated

Predicted

D1

D2

D3

D4

5HT

1A5H

T1B

5HT

1D5H

T1E

5HT

1F5H

T2A

5HT

2B5H

T2C

5HT

65H

T7

1A 2A 2B 2C 1 2 H1

ORG5222ZotepineFluparoxanOlanzapine >9Clozapine 8 - 9S16924 7 - 8

S18327 6 - 7

Amperozide <6

GGR218231

Sertindole

MDL100,907

Haloperidol

Tiospirone

Raclopride

Fluspirilene

Ocaperidone

Risperidone

S33084

L741626

Seroquel

Yohimbine

Ziprasidone

Pipamperone

©Maris Lapinsh 2002

Lapinsh et al, Mol.Pharm., 2002.

Output of PLS modelling:

©Maris Lapinsh 2002

Lapinsh et al, Mol.Pharm., 2002.

0.00

0.02

0.04

0.06

0.08

0.10

0.12dryTM1

dryTM2dryTM3

dryTM4

dryTM5

dryTM6

dryTM7

oTM1

oTM2

oTM3oTM4oTM5

oTM6

oTM7

n1TM1

n1TM2

n1TM3

n1TM4

n1TM5

n1TM6n1TM7

-0.06

-0.04

-0.02

0.00

0.02

0.04

0.06dryTM1

dryTM2dryTM3

dryTM4

dryTM5

dryTM6

dryTM7

oTM1

oTM2

oTM3oTM4oTM5

oTM6

oTM7

n1TM1

n1TM2

n1TM3

n1TM4

n1TM5

n1TM6n1TM7

Average affinity Selectivity

Properties important for ligands

Output of PLS modelling:

©Maris Lapinsh 2002

Lapinsh et al, Biochim. Biophys. Acta, 2001.

Output of PLS modelling:

©Maris Lapinsh 2002

Lapinsh et al, Biochim. Biophys. Acta, 2001.

Output of PLS modelling:Haloperidol

dryTM1dryTM2

dryTM3

dryTM4

dryTM5

dryTM6

dryTM7

oTM1

oTM2

oTM3oTM4oTM5

oTM6

oTM7

n1TM1

n1TM2

n1TM3

n1TM4

n1TM5

n1TM6n1TM7

TiospironedryTM1

dryTM2dryTM3

dryTM4

dryTM5

dryTM6

dryTM7

oTM1

oTM2oTM3

oTM4oTM5oTM6

oTM7

n1TM1

n1TM2

n1TM3

n1TM4

n1TM5

n1TM6n1TM7

Clozapine

dryTM1dryTM2

dryTM3

dryTM4

dryTM5

dryTM6

dryTM7

oTM1

oTM2

oTM3oTM4oTM5

oTM6

oTM7

n1TM1

n1TM2

n1TM3

n1TM4

n1TM5

n1TM6n1TM7

Yohimbine

dryTM1dryTM2

dryTM3

dryTM4

dryTM5

dryTM6

dryTM7

oTM1

oTM2oTM3

oTM4oTM5oTM6

oTM7

n1TM1

n1TM2

n1TM3

n1TM4

n1TM5

n1TM6n1TM7

©Maris Lapinsh 2002

Receptor sequence positions that affect interactions of each ligand

T M 1 T M 2 T M 3 T M 4 T M 5 T M 6 T M 7 A 1 A A K A I L L G V I L G G L I L F G V L G N I L V I L H Y Y I V N L A V A D L L L T S T V L P F S A I F F C N I W A A V D V L C C T A S I M G L C I I S I M A L L C V W A L S L V I S I G P L F G W R V L F S A L G S F Y L P L A I I L V M Y C R T L G I V V G C F V L C W L P F F L V M K I V F W L G Y L N S C I N P I I Y P C

D 2 D R H Y N Y Y A T L L T L L I A V I V F G N V L V C M N Y L I V S L A V A D L L V A T L V M P W V V Y L H C D I F V T L D V M M C T A S I L N L C A I S I V M I S I V W V L S F T I S C P L L F G L N V V Y S S I V S F Y V P F I V T L L V Y I K M L A I V L G V F I I C W L P F F I T H S A F T W L G Y V N S A V N P I I Y T T

5 H 2 A E K N W S A L L T A V V I I L T I A G N I L V I M N Y F L M S L A I A D M L L G F L V M P V S M L T L C A V W I Y L D V L F S T A S I M H L C A I S L L K I I A V W T I S V G I S M P I P V F G L V L I G S F V S F F I P L T I M V I T Y F L V L G I V F F L F V V M W C P F F I T N N V F V W I G Y L S S A V N P L V Y T L

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Lapinsh et al, Mol.Pharm., 2002.

Output of PLS modelling:

©Maris Lapinsh 2002

http://farm.farmbio.uu.se/maris/publ.html

Papers available at:

Maris Lapinshsupervisor Jarl Wikberg

©Maris Lapinsh 2002