11/14/2008

1

MitochondriaQSARs Involving Chemical

Effects

by Albert LeoPomona College Medicinal Chemistry Project (1969-1993)

BioByte Corp. (1993-present)

The Role of Mitochondria

in Pharmacotoxicology

• “The role of mitochondria in pharmacotoxicology:

a reevaluation of an old, newly emerging topic” (R.

Scatena, et al, Am. J. Physiol. Cell Physiol, 293,

C12-C21, 2007) points out:

1. Some antiviral nucleoside analogs display

mitochondrial toxicity by inhibiting DNA

polymerase-γ.

2. The more hydrophobic NSAIDs act as UOP.

3. Some mitochondrial toxicity of drugs depends

upon free radical production.

11/14/2008

2

Mitochondria in QSAR• 149 equations dealing with mitochondria

• 1290 unique chemical structures

• Available as a SMILES file on www.biobyte.com

• 26 equations containing 6-X-2,4-dinitro-

phenols

Beginnings of Cellular Life• In Beginnings of Cellular Life, Harold

Morowitz (Yale University Press, 1992)

says: “spontaneous formation of closed

membrane vesicles was the initiating

event in cellular evolution.”

• They maintain separate stable phases in an

aqueous environment.

• They maintain different chemical

compositions between intra- and extra-

cellular compartments.

• They maintain substantial trans-bilayer

electrical voltages, pH differences, and

oxidation potentials.

11/14/2008

3

Precursors of Chloroplasts &

Mitochondria

• The result of Intelligent Design, says Michael Behe (?)Are we

intelligent enough to refrain from injuring them?

Mitochondria

Chloroplasts

11/14/2008

4

Mitochondrial

Function

Protonophore: weak acid and hydrophobic (log P > 4)

Both ion and neutral forms in innter membrane.

Fluazinam - anti-fungal

• Set 2447:

log 1/C = 0.18 pKa – 1.57 bilin(pKa) + 0.65 log P’ +

4.67; n = 22; r2 = 0.96; OpKa = 6.96

Di-Aryl Amines as Non-Classical

Uncouplers

11/14/2008

5

X ‘Normal’ π Special’ π #Expls

2-Cl +0.72 -0.01 3

4-Cl +0.72 -0.02 3

3-CF3 +0.90 +0.01 3

2-F +0.14 -0.07 1

2-Br +0.87 -0.24 2

3-CH3 +0.51 -0.31 1

4-OCF3 +1.00 -0.18 1

• In most cases another (Y) group also present, and so 'buttressing" effect

possible.

• McGowan volume and/or CMR may help explain the difference.

Classical Uncouplers

(Protonophores)

2,4-DNP, 6-t-Bu

pKa 4.80; logP 3.55Pentachlorophenol

pKa 4.69; logP 5.12

• Set 599: I-50 respiration, rat liver mitochondria

Log 1/C = 1.73 CLOGP – 1.51 bilinCLOGP -0.51;

n = 21; r2 = 0.89; OLP =~5.6

11/14/2008

6

• Set 2257:

1/C = -0.46 pKa + 2.07 P-F + 0.76 P-P + 0.07 NVE +

12.2; n = 39; r2 = 0.96

Malonoben (SF-6847)insecticide

R = CH3 = BHT

R = P+(Ph)3 = Mito-BHT (ant-obesity

lead)

• Binds to adenine nucleotide translocase

• Lowers membrane potential (∆Ψm)

Uncouplers in Treatment of

Obesity

2,4-DNP (1930s)

11/14/2008

7

• Mitochondrial toxicity: membrane swelling and

release of Cyt-C.

Fenfluramine

N-Nitroso analog

metabolism

Pharmaceuticals with UOP

action

Amiodarone - anti-arrhythmicProtonated logD ~ 5.0; inhibits complexes 1 & II

Kebuzone - anti-rheumatic

11/14/2008

8

Capsaicin Analogs

Complex I-II

Inhibitors

• Set 6878:

log 1/C = 3.44 CLOGP – 0.28 (CLOGP)2 – 4.67

n = 6; r2 = 0.98; OLP = 6.08

Rotenone & Annonacin Analogs

Complex I-II

Inhibitors

• Set 10754:

Log 1/C = 0.14 CLOGP + 7.7; n = 5; r2 = 0.93

11/14/2008

9

4,7-subs. Acridones

Complex I-II

Inhibitors

• Set 2373:

Log 1/C = 0.74 CLOGP – 1.53 CLOGP2 – 1.36 σ4 +

3.36; n = 22; r2 = 0.90; OLP = 4.5

2,3-alkyl-Quinolones

• Set 3876:

log P = 0.73 CLOGP – 1.55

BiLinCLOGP + 1.16 I-3Me + 2.69;

n = 12; r2 = 0.96; OLP = 5.65

• Set 3877:

Log 1/C = 0.67 CLOGP – 0.93 BiLin

CLOGP - 0.35 I-Me + 1.51;

n = 13; r2 = 0.86; OLP = 5.6

11/14/2008

10

INHIBITORS OF COMPLEX

II (Succinic Dehydrogenase)

• Prototype: 3-nitropropionic acid (3-NP):

O2N-CH2-CH2-CO2H

• A natural phytoalexin; present in loco

weed (Astragalus); animal toxin.

• Human toxin in fungal-contaminated

sugar cane (China)

• Used as neurotoxin model for

Huntington's disease

Complex II-III

Inhibition

• Set 611: inhibition of succinate dehydrogenase in cinerea

botrytismold

Log 1/C = 0.58 CLOGP + 0.043 NVE – 0.219; n = 21; r2 = .88

• Set 699: acting as fungicide on rice sheath blight

Log 1/C = -19.9 MgVol + 5.3 MgVol2 + 21.7; n = 24; r2 = 0.88;

Opt.vol. = 1.9

11/14/2008

11

Complex II-III

Inhibition

• Set 1557: Benzanilides as fungicides inhibiting Complex II

Log 1/C = 1.04 CLOGP – 1.7 Bilin CLOGP -1.48 Es-X2 – B1-R2 -

1.17 σR + 1.33; n = 32; r2 = 0.89; OLP = 5.28

Complex II-III

Inhibition

• Set 1720: Thiazole-anilides as fungicides

Log 1/C = 0.64 CLOGP + 0.95 σ + 1.2 I 2,6 + 3.89; n = 42; r2 =

0.85

• I2,6 shows that di-ortho substitution is especially strong

11/14/2008

12

Complex II-III

Inhibition

• Set 2425: Carboxins inhibiting Complex II of yeast pathogen c.

laurentii

Log 1/C = -1.95 B1-4 – 0.72 σ – 1.32 I2,6 + 7.9; n = 14; r2 = 087

• In this set, 2,6-disubstitution weakens inhibitory action.

Complex IV Inhibition

• Set 1006: Inhibition of cytochrome-C from horse

heart mitochondria by alkanols (including -diols)

Log 1/C = 0.35 log P – 0.70; n = 7; r2 = 0.91

• Set 1643: Inhibition of cytochrome-C by catechols

(from same source)

Log 1/C = -5.83 σ + 2.80; n = 9; r2 = 0.97

11/14/2008

13

Complex IV Inhibition

• Set 3882: 4-quinolone analogs inhibiting bacterial

cytochrome-C

Log 1/C = 0.73 CLOGP – 0.83 bilinCLOGP + 0.53

n = 12; r2 = 0.95; OLP = 5.86

• Set 4985: Very similar relationships with cytochrome-C

from beef heart mitochondria

Log 1/C = 0.86 CLOGP – 1.29 bilinCLOGP + 2.82

n = 21; r2 = 0.90; OLP = 6.35

• Set 7095: C for maximal respiration release in rat

liver mitochondria

log 1/C = -1.33 σ - + 9.71; n = 5; r2 = 0.96

• Set 7096: C for inhibition of ATP synthesis in rat

liver mitochondria

log 1/C = -1.26 σ -- + 9.56; n = 6; r2 = 0.90

anilino-thiadiazolesInhibitors of mammary sarcomas

11/14/2008

14

Mitochondrial

Function

Protonophore: weak acid and hydrophobic (log P > 4)

Both ion and neutral forms in innter membrane.

Chloroplast ATP

Production

11/14/2008

15

Triazine inhibitors of

Plastoquinone

• Set 2252:

Log 1/C = 0.61 log P -0.96 bilinLogP -0.24 WRB-X -0.2

D-Y -0.51 T1-Y -2.8 I-Me + 8.46;

n = 47; r2 = 0.89; OLP = 4.5

Plastoquinone (atrazine target) in

chloroplasts

Ubiquinone CoQ in mitochondria

11/14/2008

16

Complex V Inhibition

• Set 8510: Salicylanilides on exchange of P with ATP in fly

mitochondria

Log 1/C = 0.056 NVE + 1.00; n = 15; r2 = 0.95

Complex V Inhibition

• Set 9574: N,N’-diphenyl thiorureas inducing maximal release of

state and respiration in rat liver mitochondria

Log 1/C = 1.91 σY = 0.54 L-X + 2.45; n = 12; r2 = 0.95

11/14/2008

17

Anilino-

Thiadiazoles

• Set 116: Rat liver mitochondria; 2-X-anilino-1,3,4-

thiadiazoles; uncoupling oxidative phosphorylation

Log 1/C = 1.01 I(CF3) -2.13 σ + 8.83; n = 11; r2 =

0.89

• Set 117: Spinach chloroplasts; 2-X-anilino-1,3,4-

thiadiazoles; uncoupling photo-phosphorylation

Log 1/C = 1.87 I(CF3) + 0.43 σ - + 3.5; n = 13; r2 =

0.9

Uncouplers in Both Mitochondria &

Chloroplasts

Pendimethalin(UOP measured; contradicts 1999 EPA manual)

Oryzalin(probable)

Trifluralin(UOP measured in plant mitochondria)

11/14/2008

18

Measurement of

Proton Gradient

(∆Ψm)

• Now available as a simple kit; e.g.

Molecular Probes B-34,950, Mitotracker

• Why not used during drug and pesticide

development? Basis for QSARs?

• MTT Assay for mitochondrial reductase:

could it be basis for QSAR?

Acknowledgements

• Dr. Gilman Veith: for his support, both moral

and financial.

• Prof. Corwin Hansch: for his skill and

persistence in accumulating and organizing

the data for so many QSARs.

• Prof. Toshio Fujita: for his insight in creating

and applying QSARs.

• Mr. Michael Medlin: for preparing the slides

for this presentation.

11/14/2008

19

11/14/2008

20

Consequence of

Mitochondrial Dysfunction

• Production of ROS (e.g. H2O2) from non-phosphorylating

respiration results in oxidative stress.

• Disability of aging most commonly ascribed to this oxidative

stress

• mDNA not as well protected nor as easily repaired as nDNA

• Mit.-dysfunction signaled to nucleus via RR (retrograde

response) but this fails thru extensive use.

• In simpler life forms (yeast, C.elegans) a deficiency in

complex IV (cytochrome-c) lengthens life span, but "quality of

life" not a concern.

• Could be a major factor in degenerative

diseases: Parkinson's, Alzheimer's, neuropathy, myopathy,

Type II Diabetes. etc.