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Generics Perspective:

Success Strategies for Genotoxic Impurity

Identification, Assessment and Control

Raphael Nudelman, Ph.D.

Head of Chemical &

Computational Toxicology

Genotoxic Impurities

London, June 2015

§ Understand the basis of the strategy used for GTI

identification, assessment and control

§ Outline key pitfalls and how they are overcome

§ Examine how we use in silico tools and (Q)SAR as part

of the assessment strategy

§ Identify how ICH M7 impacts GTI assessment strategies

Scope

Who we are

�3

Global R&D

Discovery and Product Development

Non Clinical Development

Non Clinical Safety

Raphael Nudelman

Chemical & Computational Toxicology

Generics

R&D

Specialty

R&DAPI units EHS

Who we are

� For DS

� Examine entire RoS (manual + computational) to

identify PGIs

• sm, reagents, solvents, intermediates, byproducts, products

� Assess actual + reasonably expected PGIs

� Calculate purge factors

� Control recommendations

A + B

D

E + F

G

C

Strategy

� For DP

� Identify potentially reactive degradation products

(real + potential)

� Control recommendations

Strategy

StrategyControl recommendations

� Compound specific limit (Class 1)

� TTC (Class 2 + 3)

� ICH Q3 (Class 4 + 5)

� LTL adjusted TTC

� Purgeability (no control)

� Justifiable higher exposure

• Metabolites

• Food-related

• Pharmacopoeial levels

• Reference listed drug (RLD)

• Chemical class mitigation / read-across

� Monofunctional alkyl chlorides (halides?)

� α,β-Unsaturated aldehydes (ketones, esters, amides?)

� Alkyl sulfonates?

• Advanced cancer treatment

• Tox data (in vivo mutagenicity/carcinogenicity)

StrategyControl recommendations

� When levels can’t be justified we recommend:

� Ames test

� Alternative in vivo mutagenicity studies

StrategyOther recommendations

Pitfalls

� Identifying potentially reactive structures

� Initial analysis based on structurally alerting

functional groups from Müller (2006)

Müller et al., Reg Tox Pharm 2006, 44, 198-211

Pitfalls

� Identifying potentially reactive structures

� Initial analysis based on structurally alerting

functional groups from Müller (2006)

� Subsequent in silico predictions are much more

regioselective, thus precluding PGIs identified

manually, and conversely often identify many more

PGIs

Pitfalls

� Identifying potentially reactive structures

� Initial analysis based on structurally alerting

functional groups from Müller (2006)

� Subsequent in silico predictions are much more

regioselective, thus precluding PGIs identified

manually, and conversely often identify many more

PGIs

� Solution: involve ChemTox as early as possible

Using in silico tools

� Prior to M7

� Use one in silico tool

� Result: potential for false negatives

� Post M7

� Use 2 complementary in silico tools

� Statistical based tool has too many false positives

� Conflicting predictions

“6. HAZARD ASSESSMENT ELEMENTS

===.

===.

If warranted, the outcome of any computer system-based

analysis can be reviewed with the use of expert

knowledge in order to provide additional supportive

evidence on relevance of any positive, negative, conflicting

or inconclusive prediction and provide a rationale to

support the final conclusion.”

Using in silico tools

Using in silico tools

Case studies requiring expert analysis

CompoundDerek

alert

Sarah

alertConsensus Remarks

Control

recommendation

Adipic acid

Inactive Negative

(100%

confidence)

Negative Negative Ames

test (Toxnet)

ICH Q3A

qualification

threshold

Plausible

(potential

alkylating

agent)

Positive

(alkyl

halide)

Positive Monofunctional

alkyl halide

(note 5 in M7)

TTCx10

15 µg/day

or run Ames test

Using in silico tools

Compound

Derek alert

for

mutagenicity

Sarah alertConsensus

PredictionRemarks

Control

recommendation

Benzyl chloride

Plausible

(potential

alkylating

agent)

Positive

(100%

confidence)

Positive

Positive Ames test

(Toxnet).

Mutagenic

carcinogen (Class

1) with harmonic

mean TD50

of 61.5

mg/kg/day in the

Carcinogenic

Potency Database

(CPDB)

Compound

specific threshold

of 61.5

µg/person/day is

calculated by

linear

extrapolation from

the TD50

Benzyl bromide

Plausible

(potential

alkylating

agent)

Positive

(100%

confidence)

PositiveNegative in 2-year

carcinogenicity

study

ICH Q3A

qualification

threshold

Using in silico tools

CompoundDerek alert for

mutagenicity

Sarah

alert

Consensus

PredictionRemarks

Control

recommendation

Inactive Positive Equivocal -TTC

or run Ames test

Phosphorus

oxychloride

InactiveOutside

domainEquivocal

Purge knowledge

may be used to

avoid analytical

testing

TTC

if not purged out

Using in silico tools

CompoundDerek alert for

mutagenicity

Sarah

alert

Consensus

PredictionRemarks

Control

recommendation

Diisopropyl

azodicarboxylate

(DIAD)

Inactive Outside

domainNegative

Sarah Nexus could not

associate an

appropriate training set

to this compound and

thus considered it “out

of domain”. Further

expert evaluation of

this compound showed

no structural alerts.

ICH Q3A

qualification

threshold

1,3-

Difluorobenzene

Inactive Positive EquivocalThis compound

is a class 3 impurity

TTC

or run Ames test

Using in silico tools

F

F

Compound

Derek alert

for

mutagenicity

Sarah

alert

Consensus

PredictionRemarks

Control

recommendation

4,6-Dichloro-2-

methylpyrimidine

Inactive Positive Negative

The positive Sarah alert

can be dismissed because

the training set

compounds contain alkyl

halides moieties which

are known mutagens, and

are not present in this

compound.

ICH Q3A

qualification

threshold

1-indanoneInactive Positive Negative

The positive Sarah alert

can be dismissed because

the training set

compounds contain

PAHs which are known

mutagens, and are not

present in this

compound.

ICH Q3A

qualification

threshold

Using in silico tools

CompoundDerek alert for

mutagenicity

Sarah

alert

Consensus

PredictionRemarks

Control

recommendation

THP-protected

intermediate

Inactive in bacterium;

Plausible in mammal

(alkyl aldehyde

precursor)

Negative Negative

The plausible

alert for

mutagenicity in

mammalian cells

is out of the scope

of the ICH M7

guideline

ICH Q3A

qualification

threshold

Using in silico tools

Compound

Derek alert

for

mutagenicity

Sarah

alert

Consensus

PredictionRemarks

Control

recommendation

Inactive Positive Negative

1. The examples in the

training set contain

alerting moieties that

are not present here.

2. α,β -Unsaturated

ketones are rarely

mutagenic*

ICH Q3A

qualification

threshold

Plausible

(α,β -

unsaturated

aldehyde)

Positive Positive -TTC

or run Ames test

Using in silico tools

*Snodin & McCrossen, Regul. Toxicol. Pharmacol., 2013, 67, 299-316

§ Strategy used for GTI identification, assessment

and control

§ Key pitfalls and how they are overcome

§ How we use in silico tools as part of the

assessment strategy

§ How ICH M7 impacts GTI assessment strategies

Summary