DNA binding by OECD profiler:

The true negative rate (specificity) for the “DNA binding by OECD” profiler was, to some extent, less than acceptable at 62%. The poorer performance was also reflected in the MCC value of 0.32 which was the second lowest value amongst the six profilers. Six alerts in this profiler showed low PPV including one through the acylation mechanism (1,1-dihaloalkanes), three alerts for the Michael addition mechanism (furan, α,β−unsaturated ester, α,β-unsaturated ketone), one Schiff base former mechanism (mono aldehyde) and two alerts for unimolecular aliphatic nucleophilic substitution SN1 reactions (aromatic phenyl urea and aliphatic tertiary

amines). Of the six alerts with low PPV, that for aliphatic tertiary amines was the most triggered hitting 218 substances. However, this alert falsely predicted 149 positives out of 218 with only 30% PPV, as shown in Table 3.11. The alert for aliphatic tertiary amines was described in this profiler as relating to a mechanism of action whereby P450 metabolism converts the aliphatic tertiary amine to a reactive iminium species. This has been suggested as a potential pathway to DNA adducts via an SN1 mechanism, the reaction shown in Figure 3.9 (Kalgutkar and Soglia,

2005). The relatively unspecific nature of the chemical relationship supporting this structural alert seems to be broad, this results in many false positive predictions and eventually lower accuracy of the overall profiler.

Figure 3.9. DNA adduct formation mechanism of aliphatic tertiary amine (Kalgutkar and Soglia, 2005)

Chapter 3 Table 3.11. Positive predictivity analysis for DNA binding by OECD profiler

DNA binding by OECD TOT

AL T P

FP PP V Acylation|Acylation >> Direct Addition of an Acyl Halide|Acylation >> Direct

Addition of an Acyl Halide >> Acyl halide

18 16 2 0.9 Acylation|Acylation >> Isocyanates and Isothiocyanates|Acylation >> Isocyanates

and Isothiocyanates >> Isocyanates

11 7 4 0.6 Acylation|Acylation >> Isocyanates and Isothiocyanates|Acylation >> Isocyanates

and Isothiocyanates >> Isothiocyanates

2 2 0 1.0 Acylation|Acylation >> P450 Mediated Activation to Acyl Halides|Acylation >>

P450 Mediated Activation to Acyl Halides >> 1,1-Dihaloalkanes

16 4 12 0.3 Acylation|Acylation >> P450 Mediated Activation to Isocyanates or

Isothiocyanates|Acylation >> P450 Mediated Activation to Isocyanates or Isothiocyanates >> Formamides

7 5 2 0.7

Michael addition|Michael addition >> P450 Mediated Activation of Heterocyclic Ring Systems|Michael addition >> P450 Mediated Activation of Heterocyclic Ring Systems >> Furans

20 7 13 0.4

Michael addition|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals >> 5-alkoxyindoles

4 1 3 0.3

Michael addition|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals >> Alkyl phenols

41 23 18 0.6

Michael addition|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals >> Arenes

119 55 64 0.5

Michael addition|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals >> Hydroquinones

87 42 45 0.5

Michael addition|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals >> Methylenedioxyphenyl

8 2 6 0.3

Michael addition|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals|Michael addition >> P450 Mediated Activation to Quinones and Quinone-type Chemicals >> Polycyclic (PAHs) and heterocyclic (HACs) aromatic hydrocarbons-Michael addition

Chapter 3 Michael addition|Michael addition >> Polarised Alkenes-Michael addition|Michael

addition >> Polarised Alkenes-Michael addition >> Alpha, beta- unsaturated aldehydes

23 15 8 0.7

Michael addition|Michael addition >> Polarised Alkenes-Michael addition|Michael addition >> Polarised Alkenes-Michael addition >> Alpha, beta- unsaturated amides

4 1 3 0.3

Michael addition|Michael addition >> Polarised Alkenes-Michael addition|Michael addition >> Polarised Alkenes-Michael addition >> Alpha, beta- unsaturated esters

55 9 46 0.2 Michael addition|Michael addition >> Polarised Alkenes-Michael addition|Michael

addition >> Polarised Alkenes-Michael addition >> Alpha, beta- unsaturated ketones

24 9 15 0.4

Michael addition|Michael addition >> Polarised Azo Compounds|Michael addition >> Polarised Azo Compounds >> Azocarbonamides

1 1 0 1.0 Michael addition|Michael addition >> Quinones and Quinone-type

Chemicals|Michael addition >> Quinones and Quinone-type Chemicals >> Quinones

16 14 2 0.9

Schiff base formers|Schiff base formers >> Chemicals Activated by P450 to Glyoxal |Schiff base formers >> Chemicals Activated by P450 to Glyoxal >> Ethanolamines (including morpholine)|Schiff base formers >> Chemicals Activated by P450 to Glyoxal >> Ethylenediamines (including piperazine)

1 1 0 1.0

Schiff base formers|Schiff base formers >> Chemicals Activated by P450 to Glyoxal |Schiff base formers >> Chemicals Activated by P450 to Glyoxal >> Ethanolamines (including morpholine)

4 0 4 0.0

Schiff base formers|Schiff base formers >> Direct Acting Schiff Base

Formers|Schiff base formers >> Direct Acting Schiff Base Formers >> Alpha-beta- dicarbonyl

10 7 3 0.7

Schiff base formers|Schiff base formers >> Direct Acting Schiff Base Formers|Schiff base formers >> Direct Acting Schiff Base Formers >> Mono aldehydes

35 15 20 0.4

SN1|SN1 >> Carbenium Ion Formation|SN1 >> Carbenium Ion Formation >> Aliphatic N-Nitro

11 10 1 0.9 SN1|SN1 >> Carbenium Ion Formation|SN1 >> Carbenium Ion Formation >>

Allyl benzenes

6 3 3 0.5 SN1|SN1 >> Carbenium Ion Formation|SN1 >> Carbenium Ion Formation >>

Polycyclic (PAHs) and heterocyclic (HACs) aromatic hydrocarbons-SN1

110 10 3

7 0.9 SN1|SN1 >> Iminium Ion Formation|SN1 >> Iminium Ion Formation >> Aliphatic

tertiary amines

218 69 149 0.3 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >> 30 14 16 0.5

Chapter 3 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Aromatic N-hydroxylamines

27 24 3 0.9 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Aromatic nitro

481 39 6

85 0.8 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Aromatic phenylureas

10 2 8 0.2 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Aromatic nitroso

21 21 0 1.0 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Primary (unsaturated) heterocyclic amine

66 53 13 0.8 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Primary aromatic amine

265 18 9

76 0.7 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Secondary (unsaturated) heterocyclic amine

11 1 10 0.1 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Secondary aromatic amine

34 16 18 0.5 SN1|SN1 >> Nitrenium Ion formation|SN1 >> Nitrenium Ion formation >>

Tertiary aromatic amine

59 36 23 0.6 SN2|SN2 >> Direct Acting Epoxides and related|SN2 >> Direct Acting Epoxides

and related >> Aziridines

36 35 1 1.0 SN2|SN2 >> Direct Acting Epoxides and related|SN2 >> Direct Acting Epoxides

and related >> Epoxides

184 14 4

40 0.8 SN2|SN2 >> Direct Acting Epoxides and related|SN2 >> Direct Acting Epoxides

and related >> Sulfuranes

3 1 2 0.3 SN2|SN2 >> Episulfonium Ion Formation|SN2 >> Episulfonium Ion Formation >>

1,2-Dihaloalkanes

27 23 4 0.9 SN2|SN2 >> Epoxidation of Aliphatic Alkenes|SN2 >> Epoxidation of Aliphatic

Alkenes >> Halogenated polarised alkenes

14 8 6 0.6 SN2|SN2 >> SN2 at an sp3 Carbon atom|SN2 >> SN2 at an sp3 Carbon atom >>

Aliphatic halides

103 80 23 0.8 SN2|SN2 >> SN2 at an sp3 Carbon atom|SN2 >> SN2 at an sp3 Carbon atom >>

Phosphonic esters

5 0 5 0.0 Total = number of substances flagged by alert , TP= True positive (mutagens identified positive by alert) , FP= False positive ( non-mutagens identified positive by alert) , PPV= Positive Predictivity value