PBT profiling of pre-registered substances – by QSAR ... - REACh

PBT profiling of pre-registered substances – 

by QSAR methods & 

determination of QSARs Applicability domain 

Klaus Daginnus 

Institute for Health & Consumer Protection 

Joint Research Centre, European Commission 

UBA, Dessau 10 Juli 

http://ecb.jrc.ec.europa.eu/qsar/ 

1. Computational toxicology at the JRC 

2. Inventory of pre-registered chemicals 

3. PBT- screening criteria 

4. QSARs and their applicability domain for PBT screening 

5. Conclusions 

Outline of the presentation 

1 

2

European Commission 

Directorates-General 

Directorates or Institutes 

Units 

Europeans Commissions 

Joint Research Centre 

Molecular Biology 

In Vitro Methods 

Nanobiosciences 

Chemical Assessment & 

Testing 

Systems Toxicology 

JRC 

Computational Toxicology 

Genetically Modified Organisms 

Alternative Methods & ECVAM 

Nanotechnology 

Policy 

Health and Environment Areas 

Consumer Products & Nutrition 

Overall aim: to promote the development, assessment, acceptance 

and implementation of computer-based methods potentially suitable 

for the regulatory assessment of chemicals 

Applications: REACH, Water Framework Directive, Cosmetics 

Directive, Biocides Directive, Plant Protection Products Directive 

Main approaches: SAR, QSAR, molecular modelling, ranking 

Computational methods provide information for use in hazard and 

risk assessment → “non-testing” or alternative methods 

http://ecb.jrc.ec.europa.eu/qsar/ 

3 

4

A (Q)SAR should be associated with the following information: 

1. a defined endpoint 

2. an unambiguous algorithm 

QSAR Reporting Formats QMRF 

QMRF captures information on fulfilment of OECD validation principles, 

but no judgement or “validity statement” is included 

3. a defined applicability domain 

4. appropriate measures of goodness-of-fit, robustness and 

predictivity 

5. a mechanistic interpretation, if possible 

• Principles adopted by 37th Joint Meeting of Chemicals Committee and 

Working Party on Chemicals, Pesticides & Biotechnology; 17-19 Nov 2004 

• ECB preliminary Guidance Document published in Nov 2005 

• OECD Guidance Document published in Feb 2007 

• OECD Guidance summarised in REACH guidance (IR and CSA) 

PRS – Inventory Production 

http://ecb.jrc.ec.europa.eu/qsar/information-sources/prs_inventory/ 

5 

6

TSCA (CAS overlap) 

N, 1.4, 7% 

FootPrint 

DSSTOX 

2018 

2013 

2010 

records 

PRS Statistics 

PRS_Inventory & availability of experimental data 

1023 

1059 

6019 

6067 

8848 

Atommic properties "Mean" organic PRS-substance 

O, 2.9, 15% 

Cl, 0.2, 1% 

S, 0.3, 2% 

P, 0.0, 0% 

F, 0.3, 2% 

29551 

36533 

35011 

28492 

37692 

59599 

54698 

80413 

143835 

0 20000 40000 60000 80000 100000 120000 140000 160000 

Br, 0.1, 0% 

All Structure 

PRS parent substances 

Atomic & Bond properties 

I, 0.0, 0% 

C, 14.6, 73% 

CanonicalTautomer 

UnknownStereoBonds 

StereoBonds 

is chiral 

N 

Stereochemistry PRS Parent_Substances 

6150 

11857 

13386 

15907 

62016 

0 10000 20000 30000 40000 50000 60000 70000 

7 

8

Assessment Persistency 

• Criteria: available half-life data collected 

under adequate conditions, criteria depend 

on environment, e.g. 

– P 40d in fresh water 

– vP 60d in fresh water 

• Screening P by EPISUITE 

– BIOWIN2 (does not biodegrade fast, probability < 0.5) + 

BIOWIN3 (ultimate biodegradation timescale prediction < 2.2) 

or 

– BIOWIN6 (does not biodegrade fast, probability < 0.5) + 

BIOWIN3 (ultimate biodegradation timescale prediction < 2.2) 

ECHA: Guidance on Information requirements and safety assessment, (R11) PBT assessment 

Assessment of Bio-accumulation 

• Criterion B: BCF > 2000 l/kg, 

• Criterion vB: BCF > 5000 l/kg 

• Screening Criterion not B/vB: by experiment 

or valid QSAR : log Kow

Toxicity Assessment 

• Criteria 

– NOEC < 0.01 mg/l 

– Substance classified as CMR 

– Other evidence of chronic toxicity 

• Screening criteria 

– Acute aquatic Toxicity < 0.1 

– Avian Toxicity < 30mg/kg food 

• Role of Non-testing data 

– “QSAR models seem not to be applicable for the definitive 

assessment of the T criteria” 

– at a screening level can be performed using data obtained from 

QSAR’s for acute aquatic toxicity 

P 

B 

T 

ECHA: Guidance on Information requirements and safety assessment, (R11) PBT assessment 

Applicability domain 


P EPISUITE Biowin N = 295 

B CAESAR N =466 

T DSSTOX N =585 

PRS- 

Inventory 

Organic Substances 

Merged 

N = 62.000 substances 

11 

12

300 

250 

200 

150 

100 

30 

25 

20 

15 

10 

50 

5 

0 

0 

30 

25 

20 

15 

10 

7 

6 

5 

4 

3 

2 

1 

0 

5 

0 

243 

201 

19.1 14.2 

Atomic properties PRS inventory N=62016 

43 

Comparison of the chemicals space 

PRS & PBT datasets by atomic properties) 

18 

1.2 2.7 8 

0.0 

8 

0.3 0.6 

N_Atoms N_Carbon N_Ntrgen N_Oxygen N_Phsphr N_Sulfur N_Halogen 

26 

8.0 

Atomic properties Aquatic Toxicity dataset N=576 

4 

0.6 

7 

1.3 

70 

3 

1 

0.0 0.1 0.5 

N_Carbon N_Ntrgen N_Oxygen N_Phsphr N_Sulfur N_Halogen 

6 

Max 

Mean 

Max 

Mean 

45 

40 

35 

30 

25 

20 

15 

10 

5 

0 

40 

N_Atoms 

30 

25 

20 

15 

10 

5 

0 

13.5 

24 

33 

N_Carbon 

7.8 

10.2 

Atomic properties BCF dataset N=466 

6 

N_Ntrgen 

0.5 

10 

N_Oxygen 

1.3 

N_Phsphr 

3 

1 0.0 0.1 

N_Sulfur 

Atomic Properties Persistence dataset N=295 

6 

0.6 

10 

1.7 

4 

27 

N_Halogen 

1.4 

1 

0.0 0.1 0.5 

N_Carbon N_Ntrgen N_Oxygen N_Phsphr N_Sulfur N_Halogen 

Comparison of chemicals space 

PRS & PBT dataset by Fragment fingerprints 

Fragments Fingerprint PRS-Inverntory N=62016 

Fragments fingerprint BCF dataset N=466 

6 

5 

4 

3 

2 

1 

0 

4.5 

4 

3.5 

3 

2.5 

2 

1.5 

1 

0.5 

0 

Fragments fingerprint aquatic toxicity dataset N=576 

Fragments Fingerprint Persistence dataset N=295 

6 

13 

14 

Max 

Mean 

Max 

Mean

Merge BIOWIN in 


Merge BIOWIN 

BIOWIN 6 & BIOWIN 3 

BIOWIN 2 & BIOWIN 3 

records 

7296 

Screening Assignment P by BIOWIN 

15471 

15454 

13856 

61914 

0 10000 20000 30000 40000 50000 60000 70000 

BIOWIN 

Applicability 

domain? 

Fragments not 

represented 

Remaining 

substances 

EPISUITE 4.0 http://www.epa.gov/oppt/exposure/pubs/episuite.htm 

Generation of JRC QSAR models 

Bioaccumulation, Aquatic Toxicity 

Software ADMET ADMET modeler 

Method : Kernel Modeler partial 

least Methodsquares Kernel partial 

Descriptors, e.g. least square 

Desriptors Constitutional 2D, total111, 321thereof 

80 

Constitutional 

fragments 

111 

descriptors 

Topological 

total 

14 

Atom type E-state 65 

Thereof Electronic fragments properties 80 73 

Topological Hydrogen bonding 14descriptors 

Atom 14type 

E-state 65 

Molecular ionization 12 

Electronic 

properties 

73 

Hydrogen bonding 

descriptors 

14 

Molecular ionization 12 

BCF JRC model 

IDENTICAL AND LOW 

VARIANCE INPUTS: 

63 Identical 

39 inputs are underrepresented 

(

Applicability domain BCF 


Fragments not represented 7247 

Fragments underrepresented 

13560 

Out of descriptors space 1924 

QSAR generated by Kernel partial least squares, 6 descriptors, ADMET modeler software 

17 

Remaining substances 41393 

Screening Assignment B JRC model 

B in applicability domain 

B 

vB in applicability 

domain 

vB 

not B 

records 

875 

1065 

831 

949 

49054 

62016 

0 10000 20000 30000 40000 50000 60000 70000 

18


Aquatic Toxicity baseline toxicity 

not classified, 

45838, 74% 

PRS Verhaar classification 

baseline toxicity, 

3566, 6% 

less inert , 1536, 

2% 

unspefic reactivity, 

10995, 18% 

specific 

mechanism, 48, 0% 

QSAR generated by Kernel partial least squares, 2 descriptors, ADMET modeler software 


Aquatic toxicity 


Fragments not represented 8358 

Fragments underrepresented 

19 

20 

15014 

Out of descriptors space 14213 

Remaining substances 33972 

QSAR generated by Kernel partial least squares, 15 descriptors, ADMET modeler software

Merge in Applicability 

domain 

Merge 

Solubility > Toxicity 

0.01 < Toxicity < 0.1 

Solubilty > Toxicity 

Toxicity < 0.01 

records 

Screening Assignment T 

results 

1419 

4042 

5227 

6547 

7989 

10589 

62016 

0 10000 20000 30000 40000 50000 60000 70000 

screened PBTs (31) 

21 

22

Screened P(v)B (280) 

Evaluation of QSAR 

against FOOTPRINT PPP 

Poor performance, but 249 from 468 data (BCF) and 560 from 1020 

(aquatic toxicity) out of defined applicability domain! 

23 

24

27 

10 

TCNES PBT group 

http://ecb.jrc.ec.europa.eu/esis/ 

PBT TCNES results 

72 

Evaluation of QSAR 

against PBT TCNES 

PBT TCNES 27 Type of substance 

11 

31 

66 

2 

0 

QSAR evaluation against PBT PBT TCNES vPvB POP 

not fulfilling 

44 

11 

39 

under evaluation 

deferred 

UVCB 

Organics 

Metal-Organics 

false negatives 

true negatives 

false positives 

true positives 

no evaluation possible 

25 

26

Conclusions 

I. Structures for PRS-Inventory have been generated and 

define the chemical space of REACH 

II. Pre-registered substances were screened for PBT properties 

I. P by EPISUITE BIOW 

II. B, T by JRC models 

III. Applicability domain of QSAR has been determined by 

I. Fragments properties 

II. Descriptors properties 

IV. Applicability domain demonstrates that QSAR models do not 

cover whole range of PRS and indicate areas for further 

testing 

V. Evaluation of the models with PPP data shows poor 

performance but that the models applicability domain does 

not cover PPP to an extent > 50% 

VI. Comparison with PBT TCNES evaluation shows good 

prediction of true negatives, but also prediction of many 

false negatives 

Thank you for your attention! 

Special thanks to 

Andrew Worth, Stefania Gotthardo (DG JRC 

Computational Toxicology) 

Andrew Yerin (ACD Labs) 

Robert Frankiewicz (Simulations+) 

Thomas Kraemer (German Federal 

Environmental Agency) 

Emilio Benfenati (CAESAR) 

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EPISUITE 

www.epa.gov/oppt/exposure/pubs/episuite.htm 

DSSTOX www.epa.gov/NCCT/dsstox/ 

CAESAR www.caesar-project.eu/ 

Footprint www.eu-footprint.org/ 

ACD Labs www.acdlabs.com/ 

Simulations+ www.simulations-plus.com/ 

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PBT profiling of pre-registered substances – by QSAR ... - REACh

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