The use of Derek Nexus to facilitate decision-making in chemical safety assessmentCase studies
Principal Scientist
Dr Donna Macmillan
Application of non-animal approaches for decision-making in chemical safety assessment10th-11th December, NC3Rs, London
Agenda
• Introduction to Lhasa Limited
• Derek Nexus
• Case studies:• Use as a screening tool in the pharmaceutical industry• Use in an ICH M7 regulatory context• Use in a defined approach for skin sensitisation
• Conclusions
Introduction to Lhasa Limited
Lhasa Limited
• Established 1983• Not-for-profit organisation • Educational charity• Headquarters in Leeds, UK• Offices in Newcastle, UK, Poznan, Poland• About 300 organisations worldwide use our software
• Pharmaceutical companies• Chemical and agrochemical companies• Personal product and cosmetic companies• Universities• Contract research organisations• Government (including regulatory) bodies• Consultants
Lhasa Limited - Products
Toxicity Prediction
Mutagenicity Prediction
Metabolism Prediction
Toxicity Database & Data Sharing
Degradation Prediction
Prediction of Impurity Purging
Derek Nexus
Derek Nexus
Case study 1: Use as a screening tool in the pharmaceutical industry
Derek Nexus in drug screening
• Widely used in initial drug development for toxicity (safety) profiling of target molecules• Between 20-30% of failures are generally attributed to safety
reasons
• Advantages include:• Fast• Not requiring synthesis of molecule• Can be applied at early stage drug development or to refine
candidate selection• Provides toxicity predictions for multiple endpoints
simultaneously
Brigo & Muster, Methods Mol Biol., 2016, 1425, 475-510
• In silico alerts followed up with in vitro (and maybe even in vivo) assays
• Local SAR models may be created in custom systems (Derek Knowledge Editor)
Derek Nexus in drug screening
Target identification
Lead identification
Lead optimisation
Candidate selection Phase 0
Drug development process
• Chemical libraries can be evaluated using Derek to provide a basic safety profile for each chemical
• Safety hazards identified but not necessarily used for decision-making at this early stage
• Relevant chemical scaffolds identified
• In silico analysis of target and off-target activities assessed
• Scaffolds with likely genetoxicity, carcinogenicity, hERGchannel blockade may be avoided at this stage
• Upon selection of a final candidate drug molecule, before moving into Phase 0 development, the main use of in silico tools is for ICH M7 compliance
Brigo & Muster, Methods Mol Biol., 2016, 1425, 475-510
Case study 2: Use in an ICH M7 regulatory context
• The use of two QSAR systems are permitted to predict the outcome of in vitro mutagenesis for a given impurity:• “The absence of structural alerts from two complementary
(Q)SAR methodologies (expert rule-based and statistical) is sufficient to conclude that the impurity is of no mutagenic concern”
• “If warranted, the outcome of any computer system-based analysis can be reviewed with the use of expert knowledge in order to provide… a rationale to support the final conclusion”
ICH M7 - Overview
Classification using 2 in silico modelsLikely to conclude positiveVery strong evidence would be needed to overturn both
predictions
UncertainLikely to conclude positive without strong evidence to
overturn a positive prediction
Likely to conclude positiveLack of a second prediction
suggests insufficient evidence to draw any other
conclusion
Prediction 1 (Derek)
Prediction 2(Sarah)
Positive
Positive
Positive
O.O.D. or equivocal
Positive
Negative
Negative
O.O.D. or equivocal
Negative
Negative
UncertainConservatively could assign as positive.
May conclude negative with strong evidence showing feature driving a ‘no prediction’ is
present in the same context in known negative examples (without deactivating features)
Likely to conclude negativeExpert review should support this conclusion – e.g. by assessing any
concerning features (misclassified, unclassified, potentially reactive...)
O.O.D. = out of domain
Barber et al. Reg. Tox. and Pharmacol. 2015, 73, 367
Expert review: Example
1-(4-hydroxyphenyl)prop-2-en-1-one95605-38-2
Review high level predictions
?
Expert Review
M7 classification
Expert review
?
Expert Review
M7 classification
• Plausible prediction – fires alert 664 for alpha, beta-unsaturated compounds
• Mutagenicity related to electronegativity and steric hindrance around the double bond
• Aryl substituents at C3 are typically negative or have reduced activity
• Negative prediction• Negative compounds mostly have an aryl substituent at
the C3 position• Most similar compound is negative, however there is no
protocol information
Expert summary
• Derek plausible prediction• No data to support overturning the prediction
• Sarah negative prediction• Many supporting examples are not relevant
?
Expert Review
M7 classification
M7 classification
?
Expert Review
M7 classification
Class 3Alerting structure
Case study 3: Use in a defined approach for skin sensitisation
The skin sensitisation AOP
Organism response
Organ response
Cellular response
20
Molecular Initiating Event Haptenation
T-cell activation
Activation of DC
Stress response
Skin sensitisation
Adverse Outcome Pathway
KE3
KE2
AO
MIE/KE1
KE4
Figure adapted from OECD 2012, The Adverse Outcome Pathway for Skin Sensitisation Initiated by Covalent Binding to Proteins Part 1: Scientific Evidence, Series on Testing and Assessment, No. 168.
Chemical structure& properties
Metabolism & penetration
Electrophilic substance
Assay
DPRA
LLNA
h-CLAT / U-SENS™ / IL-8 Luc
KeratinoSens™ / LuSens
GPMT (& Buehler) 406 (1992)
OECD TG
442D (2018)
429 (2010)
442C (2015)
442E (2018)
in vivo
in chemico / in vitro
HRIPT / HMT / patch test
MIE = Molecular Initiating EventKE = Key EventAO = Adverse Outcome
Lhasa’s hypothesis
21
• Apply exclusion criteria to chemicals based on known assay limitations and confidence in Derek predictions
• Ensures the most relevant information source(s) are used for a given chemical (class)
• Use Derek and assay(s) measuring the relevant KE until a concordant result is obtained - or a 2 out of 3 majority call
Pre-MIEKE4AO
DPRA
MIE
KeratinoSens™
LuSens
KE2 KE3
h-CLATU-SENS™IL-8 Luc
MIE = molecular initiating eventKE = Key EventAO = adverse outcome
Exclusion CriteriaExclusion Criteria Derek MIE KE2 KE3 Comment
Metabolism Prohapten ✓ ✗ ✓ ✓Assays lacking metabolic competency are
deprioritised as they are less likely to predict prohaptens well
logP> 3.5 ✓ ✓ ✓ ✗ Cell-based assays are deprioritised for
chemicals with a logP > 3.5 (KE3) and logP > 5 (KE2) as more lipophilic chemicals may
lack high solubility in these cell-based assays> 5 ✓ ✓ ✗ ✗
Lysine reactive Exclusive ✓ ✓ ✗ ✓
The Nrf2-ARE pathway is associated with cysteine binding - lysine-reactive chemicals
may not be reliably predicted
Reasoning level Equivocal ✗ N/A
Alerts with a likelihood of equivocal have less evidence of skin sensitisation potential than other likelihoods (e.g. certain) and are
thus deprioritised
Negative prediction
Misclassified features ✗ N/A Negative predictions with ‘misclassified
features’ or ‘unclassified features’ are deprioritised as these are associated with
higher uncertainty.Unclassified
features ✗ N/A
DPRA
KeratinoSens™LuSens
h-CLATU-SENS™
IL-8 Luc
Macmillan & Chilton, Reg. Tox. and Pharmacol., 2019, 101, 35
Defined approach decision tree
Potency prediction
modelNH2
NH2
1st assay
1st assay
1st assay
EquivocalNon-sensitiser with misclassified or unclassified features
2nd assay
3rd assay
2nd assay
2nd assay
2nd assay
CertainProbablePlausible
Non-sensitiserDoubted
ImprobableImpossible
Derek alert
outcomePotency category 5/6 (GHS no cat)
Query Use Derek outcome to determine decision tree branch
Prioritise in chemico/in vitro
assays using exclusion criteria
Potency category 1 (GHS 1A)Potency category 2 (GHS 1A)Potency category 3 (GHS 1B)Potency category 4 (GHS 1B)
Run in chemico/in vitro assays in order of AOP (MIE → KE2 → KE3) unless de-
prioritised by exclusion criteriaPotency prediction using
k- nearest neighbours modelHazard prediction
using ‘2 out of 3’ approach
Exclusion criteria
sensitiser
sensitiser
non-sensitiser
non-sensitiser
sensitiser
non-sensitiser
Blue italics = Derek outcomeRed arrow = positive resultGreen arrow = negative result
Macmillan & Chilton, Reg. Tox. and Pharmacol., 2019, 101, 35
Results - Hazard
BA = Balanced AccuracySe = SensitivitySp = Specificity
Macmillan & Chilton, Reg. Tox. and Pharmacol., 2019, 101, 35
Results - Potency (GHS)Defined approach prediction vs in vivo outcome
LLNAn = 174
Acc = 73%
Humann = 79
Acc = 76%
no cat no cat
no c
at
no c
at
Under-prediction
Over-prediction
Under-prediction
Over-prediction
Macmillan & Chilton, Reg. Tox. and Pharmacol., 2019, 101, 35
Conclusions
• Three case studies have shown how Derek Nexus can be used to inform decision making in chemical risk assessment.
• As a standalone tool for screening in early pharmaceuticaldiscovery
• Regulatory application where expert review of predictions isimportant (ICH M7)
• Within a defined approach, where results from in vitro assaysalso need to be considered
Acknowledgements
• Chris Barber
• Rich Williams
• Martyn Chilton