In silico Tools @ EFSA · 2020-02-02 · Exposure Assessment Hazard identification Hazard charact...
Transcript of In silico Tools @ EFSA · 2020-02-02 · Exposure Assessment Hazard identification Hazard charact...
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Jean Lou Dorne Senior Scientific Officer
Scientific Committee and Emerging Risks Unit EFSA
OpenFoodTox and other Open Source
In silico Tools @ EFSA
Summer School “In silico methods in food safety”
14th June 2017
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EFSA’s Role in Risk Analysis
Scientific Risk Assessment
Risk Communication
Risk Management
•Independent Risk Assessment
•Risk communication
Methodology Codex Alimentarius: •Hazard identification •Hazard characterisation •Exposure assessment •Risk characterisation
EFSA
Risk Manager •EC •EU Parliament •Member States •Council
Basic Principles in Chemical RA
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FROM QUESTION TO ANSWER
European Commission
European Parliament
Member States
EFSA (“self mandate”)
Question?
Risk Assessment
Opinion
Risk Management
Risk Communication
Industry
Media
Consumers
Professionals
Terms of reference Background
Basic Principles in Chemical RA
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Occurrence data
(Concentration in
food)
Risk Characterisation
CHEMICAL
Food
consumption
Health-based guidance value
Hazard Assessment
Toxicity
Benchmark Dose/ NOAEL
Exposure assessment
Probabilistic
/Deterministic
Exposure
estimates
Toxicokinetics / Toxicodynamics
Chronic Acute
MOE ADI / TDI ARfD
Uncertainty
Factor
Dorne et al, 2009- Trends in Analytical Chemistry
IN A NUTSHELL…
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PARACELSUS (1493-1541)
“All things are toxic and there is nothing
without poisonous qualities: it is only the dose
which makes something a poison”
Toxicology What the body does to a chemical and what a chemical does to the body
Toxicodynamics What a chemical does to the body
How the chemical exerts its toxicity
target receptor/cell/organ
Toxicokinetics What the body does to a chemical
How the chemical is eliminated
from the body or activated into a
toxic species (ADME)
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Main title
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DATA/EVIDENCE AVAILABLE IN CHEMICAL RA
Tier Exposure Assessment
Hazard identification
Hazard characterisation
Risk Characterisation
Occurence Consumption TK TD TK TD
0 Semi-Q
Default values No data No data
in silico Read across
Default values TTC
Read across In silico
Default UF
e.g. Default values Qualitative
1 Point
estimates
Point estimates in food
categories
In silico Limited
data Semi-Q
In silico Limited data Read across
in silico Basic TK
Read across
in silico Read across
NOAEL Default UF
e.g. Semi-quantitative
2 Measured
data
Measured in some food categories
Dossier data Qttve
Dossier Data
in silico ADME data
NOAEL/ BMDL
Default in silico
UF
e.g. Quantitative Deterministic/ Probabilistic
3 Large measured dataset
Full patterns -food categories
Dossier and/or lit. (in vitro, in vivo)
Data in dossier and/or lit. (in vitro, OMICs, epi)
MoA/AOP, Epi data, PB-PK model, BBDR, BMDL Chemical specific adjustment factor (CSAF)
e.g. Quantitative Full probabilistic
Basic Principles in Chemical RA
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DATA FROM DOSSIER: REGULATED PRODUCT
Tier Exposure Assessment
Hazard identification
Hazard characterisation
Risk Characterisation
Occurence Consumption TK TD TK TD
2 Measured
data
Measured in some food categories
Dossier
data Qttve
Dossier Data:
genotox, tox
in silico ADME data
NOAEL/ BMDL
Default UF
e.g. Quantitative Deterministic/ Probabilistic
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Tier Exposure Assessment
Hazard identification
Hazard charact
Risk Characterisation
Occurence Consumption TK TD TK TD
3 Large measured dataset
Full patterns -food categories
Human Data Biomarker excretion/blood
Human data Biomarker renal toxicity
PB-PK-BMDL (Human data) Chemical specific adjustment factor (CSAF)
e.g. Quantitative Full probabilistic
DATA-RICH CHEMICAL: CADMIUM
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Tier Exposure Assessment
Hazard identification
Hazard characterisation
Risk Characterisation
Occurence Consumption TK TD TK TD
0 Semi-Q
Default values
No data
No data in silico
Read across
Default values
TTC Read
across In silico
Default UF
e.g. Default values
Qualitative
DATA-POOR: EMERGING MYCOTOXIN
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Scientific Basis of Uncertainty Factors
OpenFoodTox: EFSA’s Open Source Hazards Database
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Catalogue of EFSA’s chemical toxicity data since creation
-Contaminants (Human and Animal health)
-Vitamins and minerals (Human health) (NDA),
-Food additives and Nutrient Sources, Food contact materials, Flavourings and processing aids (Human Health)
-Feed Additives (Human and Animal Health, Ecotoxicology)
-Pesticides (Human and Animal health, Ecotoxicology)
Easy Reference and Crisis
-One reference DB Chemical Hazards: Search easily and efficiently
-Crisis: Quick and Easy access to all EFSA’s Hazard Data
International Harmonisation
- Use OECD Harmonised Templates (OHT) for data model (ECHA/OECD)
compatible with IUCLID/ ECHA-OECD QSAR toolbox
-Search compounds by name, CAS number on e-chem portal
-Generate data sheet as summary of hazard id and charact (June 2016)
d
OPENFOODTOX: EFSA' S CHEMICAL HAZARDS DATABASE
Future Mixture RA EFSA
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WHAT DOES OPENFOODTOX CONTAIN ?
oChemical Information Information on chemical nomenclature (EU nomenclature, IUPAC, CAS... ), trade name, chemical group/panel (i.e. pesticide), chemical use (i.e fungicide), chemical structure (i.e triazoles, organophosphates….). oDocument descriptors Information on EFSA’s opinion for the specific chemical or group of chemicals. Info from EFSA ‘s RAW system (question number, mandate, number), link to the document oToxicity Endpoint/ Hazard identification Information on critical toxicity study using OECD picklists when possible (species, dose, target organ…) oCritical study to demonstrate genotoxicity status Providing essential information of critical genotoxicity study when assessed oHazard /Risk characterisation Information for health based guidance values (ADI/TDI) uncertainty factors…
Future Mixture RA EFSA
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TOWARDS AN OPENSOURCE HAZARD DATABASE
Tier Exposure Assessment
Hazard identification
Hazard characterisation
Risk Characterisation
Occurence Consumption TK TD TK TD
0 Semi-Q
Default values No data No data
in silico Read across
Default values
TTC In silico
e.g. Default values Qualitative
1 Point
estimates
Point estimates in food
categories
In silico Limited
data Semi-Q
In silico data Read
across
in silico Basic TK
Read across
in silico NOAEL
Default UF
e.g. Semi-quantitative
2 Measured
data
Measured in some food categories
Dossier data Qttve
Dossier Data
in silico ADME data
NOAEL/ BMDL
Default in silico
UF
e.g. Quantitative Deterministic/ Probabilistic
3 Large measured dataset
Full patterns -food categories
Dossier and/or lit. (in vitro, in vivo)
Dossier and/or lit. (in vitro, OMICs, Epi)
MoA/AOP, Epi data, PB-PK model, BBDR, BMDL, CSAF
e.g. Quantitative Full probabilistic
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CONTENT
1,650
Scientific
outputs
(metadata +
DOI)
4,400
Substances
(chemical
identifiers
including
SMILES) 10,000
Toxicologica
l endpoint
studies 140 Positive
genotoxicity
studies
12,000 risk
assessment
summaries
Full Download Knowledge junction: https://zenodo.org/record/344883#.WUDqK_mGPIU
Microstrategy Tool: https://dwh.efsa.europa.eu/bi/asp/Main.aspx?rwtrep=400
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Main title
Open Source in silico Tools to Quantify Toxicological
Processes
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Case studies to develop in silico tools
• QSAR model on pesticide Toxicity in bees (OpenFoodTox, US-EPA, DEMETRA DB) : Classifier
• QSAR model to predict LC50 in rainbow trout (OpenFoodTox) : Continuous model
-Physico-chem properties, structure, toxicity : R2 >0.75
• QSAR model to predict NOAEL in rats (OpenFoodTox, Fraunhofer) : Continuous model
-Physico-chem properties, structure, toxicity : R2 >0.75
Scientific report Summer 2017
• QSAR model to predict NOAEL for liver toxicity in rats (OpenFoodTox, Fraunhofer) : Continuous model
OPENFOODTOX AND IN SILICO TOOLS
Future Mixture RA EFSA
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Main title
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Main title
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Main title
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Main title
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Main title
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Future Mixture RA EFSA
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External
dose
Internal
dose
Target organ
responses
Toxic
Effect
Target organ
metabolism
Target organ
dose
External
dose
Toxic
Effect
External
dose
Internal
dose
Toxic
Effect
External
dose
Internal
dose
Toxic
Effect
Target organ
Dose
External
dose
Internal
dose
Toxic
Effect
Target organ
metabolism
Target organ
Dose
-Levels of Knowledge, Toxicokinetic and
Toxicodynamic processes
Toxicokinetics Toxicodynamics
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In vivo TK studies in animals
Blood/ tissues [C] for active substance/relevant metabolites (Cmax; AUC )
in relevant species understanding toxicity studies
Investigating entero-hepatic circulation
Comparative Animal versus human microsomes or intact cell
systems
Relevance animal tox -guide interpretation, further define testing strategy
e.g. human in vitro metabolite not in test species
Protocols available publicly incl. ECVAM work on developing TK standards
In vitro models hepatic/ non-hepatic microsomes (e.g. intestinal)
Major human metabolites (>10% of AD) not at sufficient levels in animal
studies further investigated for their toxicity profile.
New Data requirements for pesticides
Regulation 283- 284/2013 : TK Data
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MAJOR METABOLIC/EXCRETION ROUTES IN HUMANS
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MAJOR METABOLIC/EXCRETION ROUTES IN HUMANS
Phase I enzymes Cytochrome P-450, ADH, Esterases…
CYP2D6 CYP1A2
CYP2A6
CYP3A4/CYP3A5
CYP2C9
CYP2C19
CYP2E1
Phase II enzymes Conjugation reactions UDP-Glucuronyltransferases, Sulphotransferases Glutathione-s-transferases Methyl-transferases N-acetyltransferases Amino acid conjugation
Renal excretion
Transporters Phase 0- Uptake transporters: e.g OATPs, OCTs. Phase III-Efflux pumps: e.g ABCs (P-glycoproteins and MRPs)
Default UFs to CSAFs : Past, Present and Future in Food Safety
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-HUMAN VARIABILITY IN TOXICOKINETICS-
From pharmaceutical database and compounds relevant to food safety, Identify Phase O, 1, 2, 3 isoforms in vitro , excretion
data etc. PK parameters of acute and chronic exposure: Meta-
analysis Human variability distributions -isoform specific for
different subgroups of the population.
Can be refined in the future
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TK AND INTEGRATED TESTING STRATEGIES
Structure Clusters Chemical Categories/ (Q)SAR
In vitro Assays
Adverse Outcome
Toxicokinetics PB-TK
In Vitro-In Vivo Signatures
Toxicokinetics In vitro id isoforms phase I, II, transporters. Consequences of metabolism id of toxic moiety(ies) TK parameters (Vm,Km, Clint, Fu). Use human Variability in TK from historical databases and software
IVIVE
Historical TK/Tox Data Read-across…
Margin of Exposure
Exposure
Chemical Risk Assessment : data needs
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-HUMAN VARIABILITY IN TOXICOKINETICS AND UF-
From pharmaceutical database human variability in TK available for many drugs /enzyme isoforms in different subgroups of the population. Rationale for meta-analysis of TK data to derive pathway-related uncertainty factors- default distributions. Can be refined in the future
Default UFs to CSAFs : Past, Present and Future in Food Safety
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lgmjk
μjk τjk b a
lvjk
njk
τj μj
τst τsub
Substrate j
Study k
μsub
Priors μindiv τindiv
3 levels :inter-study, inter-substrate et inter-individual Variability
)1
,(~lgjjk
jkjkn
Normalm
)1²(1
~ jk
jjk
jk nChin
lv
)1
,(~st
jjk Normal
)1
,(~sub
subj Normal
)1
,(~ind
indj Normal
Amzal et Dorne, 2008
Bayesian Meta-analysis of TK data
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EM
50th percentile
95th percentile
𝑈𝐹𝐸𝑀 =𝑝95𝐸𝑀
𝑝50𝐸𝑀
50th percentile
95th percentile
EM PM
𝑈𝐹𝑃𝑀 =𝑝95𝑃𝑀
𝑝50𝐸𝑀
Polymorphic CYP2D6 Example
EM PM
(1-α) EM x + α PM x
Population
50th percentile
95th percentile
𝑈𝐹𝑝𝑜𝑝 =𝑝95𝑝𝑜𝑝
𝑝50𝑝𝑜𝑝
Monte- Carlo
Bechaux et al (in preparation)
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Main title
Lovastatin.lactone Codein Bromperidol Flecanaide Tramadol Aripiprazole Atomoxetine Nortriptyline
1.0
1.5
2.0
2.5
3.0
3.5
4.0
CL asian
ratio
EM
/IM
% Dose metabolised by CYP2D6 and differences between Extensive and poor metabolisers in Caucasian and Asian populations
Polymorphic CYP2D6 Example
Oxycodone Ramosetron Mirtazapine Mirabegron Fluoxetine Haloperidol R.S.Tramadol S.carvedilol Fesoterodine Carvedilol S.S.Tramadol R.R.Tramadol R.carvedilol Venlaxatine Metoprolol Risperidone Dextromethorphan S.Metoprolol R.Metoprolol Propafenone
02
46
810
12
AUC caucasian
ratio
EM
/PM
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Collection data physio/ biological param- calibrate TK tools
- Body weight, variability enzymes expression Gut/liver etc…
- Human Variability metabolism (CYP isoforms) and excretion using Pharmaceutical DB
- TK tools from one compartment to multi compartment/PB-PK e.g. blood/liver/gut/kidney
- Case studies 10 compounds relevant to food and feed safety combining TK and TD: regulated, contaminants
In Future Open TK tools in R (spring 2018)
In Parrallel, TK tools for 5 veterinary species (cow, pig, cat, chicken etc..) and ERA (zebra, trout, earth worm)
OPEN SOURCE TK MODELS: DATA AND MODELS
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Prototype TK Modelling Platform
Solver
Model
outputs
Compound library:
- PBTK parameters
- Physio/chemico properties
- Physio/biological
- Default values from
selected publications
PBTK model
R-based
USER
INTERFACE
Pathway variability
10 cases studies
5 pathways informed by ELS
+ additional physio/biological
parameters
C-based ext.
For faster
computation
s
Sensitivity
analyses
module
Monte Carlo
population
variability
simulator
Additional
outputs
Allometric
scaling
QSAR
QVIVE
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COMBINING VARIABILITY IN TK AND IN VITRO DATA : OPENSOURCE PLATEFORM
TK
Isoform-specific Variability Distribution : Open Source Tool
Meta-analysis TK studies (acute, chronic) and TD studies (vivo, vitro, epidemio)
Phase I and Phase II enzymes and Transporters
Isoform-specific Metabolism
In Vitro Human cell system
Combine Human TK data and Tox data
Modelled CASF
Combine Human TK data and human epi data
Combine TK data and in vitro TD data
TD
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Quantitative theory for metabolic organisation from ‘first principles’
– time, energy and mass balance
Life-cycle of the individual
– links levels of organisation: molecule ecosystems
Kooijman (2000)
Kooijman (2010)
DEB MODELS
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eggs
mobilisation
structure
somatic maintenance
growth
maturity maintenance 1-
reproduction
maturity buffer
maturation
food feces
assimilation
reserve
3-4 states 8-12 parameters
system can be scaled to remove dimension ‘energy’
What are DEB MODELS ?
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hazard rate
Chemical affects the probability to die hazard modelling
toxicokinetics
model
internal concentration
hazard
rate
NEC
blank value
survival probability
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scaled internal concentration
hazard
rate
scaled internal concentration
hazard
rate
NECNEC
blank valueblank value
killing
rat
e
0 1 2 3 4 5 6 70
0.2
0.4
0.6
0.8
1
time (days)
fracti
on
su
rviv
ing
0 1 2 3 4 5 6 70
0.2
0.4
0.6
0.8
1
time (days)
fracti
on
su
rviv
ing
Elimination rate 0.73 d-1
Blank hazard rate 0.0064 d-1
NEC 2.8 (2.1-3.1) µg/L
Killing rate 0.031 L/(µg d)
timetimetime
inte
rna
l co
ncen
tra
tio
nin
tern
al co
ncen
tra
tio
nin
tern
al co
ncen
tra
tio
n
timetimetime
inte
rna
l co
ncen
tra
tio
nin
tern
al co
ncen
tra
tio
nin
tern
al co
ncen
tra
tio
n
elim
inat
ion
rate
Example
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CAT EVOLUTION , HYPERCANIVORY AND DIET
Integrating Toxicokinetics in Risk Assessment
Cat in UGT enzymes (hypercanivory)
no induction by plant compounds
Lacking
-Glycine conjugation
-N-acetyltarnsferases
-Thiopurine s-methyltransferases
In context of Ecological RA and
endangered species can we predict
toxicity using physico-chemcial
properties, structure ?
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-Building Open source TK and DEB tools-
External
dose
Internal
dose
Target organ
responses
Toxic
Response
Target organ
metabolism
Target organ
dose
FAT
LUNG BLOOD
ALVEOLAR SPACE
POORLY-
PERFUSED
TISSUES
C alv
C art
Q alv
C art
C art
Q c
Q f
Q s
Q alv C inh
Q c C ven
C vf
C vs
C = C / P vf f f
C = C / P vs s s
LIVER
METABOLISM
V max K m
C art
Q l C vl
C = C / P vl l l
,
RICHLY-PERFUSED
TISSUES
C art
Q r C vr
C = C / P vr r r
Vf
Vs
Vr
Vl
PB-TK models DEB Models
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Main title
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45
CONCLUSION AND RECOMMENDATIONS
OpenFoodTox provide historical data from EFSA RA
Human, animal helath and Eccological RA
QSAR models developed from OpenFoodTox support 3Rs
Open Source TK models to integrate exposure (external) to TK (internal) and Toxicity by 2018
Open Source DEB models: Taxa-specific data to link internal dose to toxicity by 2018
TK/TD platform: Integration of population variability in TK and TD processes for RA (by 2020-2021)
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THANKS TO PARTNERS
OpenFoodTox: S-IN : Vicenza, Italy
QSAR models : Istituto Mario Negri, Milan, italy
TK platform: 1.Laser Analytica, Paris, France
2. INERIS, Paris, France
3.Radboud University, Niemigen, The Netherlands
TK/TD platform: 1.ANSES, Paris, France
2. ISS, Rome, Italy
3.University of Utrecht, UtrechtThe Netherlands
4.University of Bretagne, Brest, France
DEB Models 1.Center for Ecology and Hydrology , UK
2. Technico Lisboa, Lisbon, Portugal
3.Akvaplan Niva, Tromso, Norway
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Many Thanks
Questions ?