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Ames/QSAR international collaborative project
Masamitsu Honma, Ph.D.Division of Genetics and Mutagenesis,National Institute of Health Sciences,
Kanagawa, JAPAN
The Use of QSAR in ICH-M7 Guideline for Assessment of Genotoxic Impurities
Two (Q)SAR prediction methodologies that complement each other should be applied. One methodology should be expert rule based and the second methodology should be statistical based.
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, and no further testing is recommended.
How to Improve QSAR Prediction ?
New QSAR Algorithm/ Model• AI, Deep-learning ?
Training data set• New• Many• Reliable
Chemicals newly manufacturing produced or imported more than 100kg/year must be assessed its mutagenicity by Ames assay.
Industrial Safety and Health Law “An-eihou” in Japan
The permission of the use of the Ames data to improve QSAR models by Chemical Hazards Control Division, Industrial Safety and Health Department, Labor Standards Bureau in MHLW
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Manufacture
import
Proposal of International Collaborative Studies to Improve
Ames/QSAR models (QSAR2014, Milan, Italy, June 2014)
1. Lhasa Limited (UK)
2. MultiCASE Inc (USA)
3. Leadscope Inc (USA)
4. Istituto di Ricerche Farmacologiche Mario Negiri (Italy)
5. LMC-Bourgas University (Bulgaria)
6. Istituto Superiore di Sanita (Italy)
4. Prous Institute (Spain)
5. Swedish Toxicology Science Research Center (Sweden)
9. FUJITSU KYUSHU SYSTEMS (Japan)
10. IdeaConsult Ltd. (Bulgaria)
11. Molecular Networks GmbH and Altamira LLC (USA)
12. Sumilation Plus (USA)
DEREK Nexus, SARAH
CASE Ultra rule-, statistical-based
Leadscope rule-, statistical-based
CAESER, SARPY, kNN
TIMES/AMES
Toxtree
Symmetry
AZAMES
ADMEWORKS
AMBIT
ChemiTunes and ToxGPS
Mut_Risk-0
QSAR Venders QSAR Model
Participants in Ames/QSAR Project
Ames Mutagenicity of Challenging Chemicals
Class A : Strongly positive, in which the chemical generally induces more than 1,000 colonies/mg in at least one Ames strains in the presence or absence of rat S9.
Class B : Positive, in which the chemical induces colonies more than 2-fold of the negative control at least one Ames strains in the presence or absence of rat S9, but not in class A.
Class C : Negative, which is neither class A nor B.
Category
Class A
Class B
Class C
Total
Phase I(2014-2015)
183 (4.7%)
383 (9.8%)
3,336 (85.5%)
3,902
Phase II(2015-2016)
253 (6.6%)
309 (8.1%)
3,267 (85.3%)
3,829
Phase III(2016-2017)
236 (5.4%)
393(8.9%)
3,780 (85.7%)
4,409
Total(2014-2017)
672 (5.5%)
1,085 (8.9%)
10,383 (85.6%)
12,140
Ames/QSAR Project (Phase I-III) Challenged Chemicals
100-Specificity (%)
Sens
itivi
ty (%
)
ROC Graphs for Challenged QSAR Models’ Validation
0
20
40
60
80
100
0
20
40
60
80
100
0 20 40 60 80 100 0 20 40 60 80 100 0 20 40 60 80 100
Validation I(A vs. C)
Validation II(A vs. C)
Validation III(A vs. C)
Validation I(AB vs. C)
Validation II(AB vs. C)
Validation III(AB vs. C)
CH3
N
H2N
Cl
Cl
O
Cl Cl
H
H3C
NH
O
O
O
CH3
OH
O
NH2
O
O
NH2OH
HO
H2N
HO
OH
NH2
CH
3
CH
3
CH
3
HC
CH3N
CH3
P
NH3CCH3
N
CH3
CH3
Cl
Cl
O
F F
F
FN
F
F
FCH3
P
Cl
Cl
H3CS
S NH
N
HNH
O
F F
F
NH
H
O
O
OCH3
OHO
CH3
O
OCH3
SO
O
Cl
H3C O
O
NH2 HCl
N
N
Cl
Cl
O
F
Cl
CH3
S
O
O Cl
CH3
CH3
Br
O
CH2
CH3H3C
CH3
False NegativesClass A chemicals, but negative call by almost QSAR tools
HH3C N
H
HH
O
OH3C
OF
F
FF
CH
F
FF
CH3
H3C
O
Cl
N
O
O
O O Br
Br
F
N
O
O
N N
O
FCl
O
O
N
F
F
O
O
F
O
N
O
ON
F
False PositiveClass C chemicals, but positive call by almost QSAR tools
O
N
O O
O
OO
O
H2N
O– N
+
O
O
O
N
N
NN
Cl
N +
OO–
Cl
H3C O
N+
O
O–
NH
O
N+
O
O–
O
N+
O
O–
O
N+
O
O–
O–
N+ O
O
O
N+
O–
O
HO
NN
HO
N+
O–
ON+
O–
O
O
NH
NH2
O
OH NOO
N
CH3
O O
NO
O
O
OCH3
H3C
N
NO O
N
N
CH3
N N
O
O
N
O
N
NH2
ClO
O
O
N
S
NO
O
O
N O
NO O
O
O
O
N
NO
OO
O O
O
O
N
NOO
O
O
O
O
OThey may be mutagens?
What means Ames positive?
Class A : Strongly positive, in which the chemical generally induces more than 1,000 colonies/mg in at least one Ames strains in the presence or absence of rat S9.
Class B : Positive, in which the chemical induces colonies more than 2-fold of the negative control at least one Ames strains in the presence or absence of rat S9, but not in class A.
Class C : Negative, which is neither class A nor B.
may contain false-positive.
may contain false-negative.
Is this Ames Positive?-Example A-
Confidential
Confidential
TA100 (+S9) 1st trial
Negative
TA100 (+S9) 2nd trial
Negative
TA98 (+S9) 1st trial
Negative
TA98 (+S9) 2nd trial
Negative
TA98 (+S9) 3rd trial
Negative
QSAR Tools Results
Derek NX INACTIVE
CASE UltraPHARM_SALM
Positive
QSAR Tools Results
Derek NX PLAUSIBLE
CASE UltraPHARM_SALM
Positive
4'-(chloroacetyl) acaetanilde
(Cas# 140-49-8)
O N
O
Cl
Is this Ames Positive?-Example B-
TA1537(-S9)
TA1537(+S9)
Lab. A Lab. B Lab. C Lab. D
Dunkel et al., Environ Mutagen, 7, Suppl. 5, 1-248 (1985)
Positive
QSAR Tools Results
Derek NX INACTIVE
CASE UltraPHARM_SALM
Negative
StructureAmesResult
Derek_NXver.4.0.5 Sarah
CASE UltraStatistical-
based
CASE UltraGT_EXPERT
Leadscope ICHM7 statistical-
based
Leadscope ICHM7 rule-based CAESAR SARPY TIMES/AMES Toxtree AZAMES ADMEWORKS AMBIT ChemiTunes MUT_Risk-0
C Posotive Positive Positive Positive Posotive others Positive Posotive Negative Positive Posotive N/A(1) Ambiguous Posotive Posotive
C Posotive Negative Positive Positive Posotive others Positive Posotive Posotive Positive Negative Posotive Negative Posotive other
C Posotive Positive Positive Positive Posotive others Positive Posotive Negative Positive unsure ? Positive Posotive Posotive
C Posotive Equivocal Positive Positive others others Positive Posotive Negative Positive positive ? Negative Posotive Posotive
C Posotive Negative Positive Positive Posotive others Positive Posotive positive Positive positive ? Positive Posotive Posotive
C Posotive Positive Positive Positive Posotive others Positive Posotive Negative Positive positive Posotive Ambiguous Posotive Posotive
HCl
NH 2
H 2 N N
ClO
FF
Cl O
FF
S
Cl
OO
CH3
O
Cl
O CH3
N
O
CH3
Cl
O
NH2
SO O
Cl
Cl
O
CH 3
Cl
O
Cl
O
N
NN
N
Org. Process Res. Dev., 2015, 19 (11), pp 1495–1506DOI: 10.1021/acs.oprd.5b00106
False Positive in Carboxylic and Sulfonic Acid Halides
Integrated approach for Genotoxicity Assessment
QSAR is not only a tool for the prediction. It can support to judge the results of actual Ames test.
Molecular Mechanism Mutagenic Potential
HO
HN
O
Cl
Cross-Talk
Re-modeling
Re-build Data Base
Feed-Back
QSAR beyond Ames
Summary
A large number of highly reliable data sets are essential to allow the development and improvement of QSAR models.
The Ames/QSAR international collaborative study is successfully ongoing. Its outcome gives a lot of benefits to QSAR vendors, QSAR users, and regulatory.
The integrated approach with QSAR results increases the sensitivity and specificity of the Ames test. It can support to judge the Ames results with molecular mechanism.
Web-Site of AMES/QSAR International Collaborative Study
AMES QSAR
The next Ames/QSAR challenge program will start from the end of 2018. Not only QSAR vendors, but also academia and IT companies are welcome to join the challenge. Hopefully, new QSAR models using AI and deep-learning will challenge.
AcknowledgementNational Institute of Health Sciences (Japan)
Airi KitazawaMasami YamadaTakeshi MoritaMakoto Hayashi
Lhasa Limited (UK)
MultiCASE Inc (USA)
Leadscope Inc (USA)
Prous Institute (Spain)
Bourgas University (Bulgaria)
Istituto Superiore di Sanita (Italy)
Istituto di Ricerche Farmacologiche Mario Negiri (Italy)
Swedish Toxicology Sciences Research Center (Sweden)
FUJITSU KYUSHU SYSTEMS (Japan)
IdeaConsult Ltd. (Bulgaria)
Molecular Networks GmbH and Altamira LLC (USA)
Sumilation Plus (USA)
Alex Cayley
Roustem Saiakhov
Glenn Matt
Christine DeMeo
Ovanes Mekenyan
Cecillia Bossa
Emilio Benfenati
Ulf Norinder
Hitomi Koga
Nina Jelazkova
Chihae Yang
Bob Clark
Chemical Hazards Control Division, Labor Standards Bureau in MHLW (Japan)
Kazuyo OofuchiShinji TsunodaHideaki HirakawaShinji KouzukiTatsuya Anai
Pharmaceutical Medical Devices Agency (Japan) Jun-ichi FukuchiKeiji Hirabayashi
