1. Mitochondria QSARs Involving Chemical Effects
by Albert Leo
Pomona College Medicinal Chemistry Project ( )
BioByte Corp. (1993-present)

2. 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:
Some antiviral nucleoside analogs display mitochondrial toxicity by inhibiting DNA polymerase-γ.
The more hydrophobic NSAIDs act as UOP.
Some mitochondrial toxicity of drugs depends upon free radical production.

3. Mitochondria in QSAR 149 equations dealing with mitochondria
1290 unique chemical structures
Available as a SMILES file on
26 equations containing 6-X-2,4-dinitro- phenols

4. 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.

5. Precursors of Chloroplasts & Mitochondria

6. Mitochondria Chloroplasts
The result of Intelligent Design, says Michael Behe (?)Are we intelligent enough to refrain from injuring them?

7. Mitochondrial Function
Protonophore: weak acid and hydrophobic (log P > 4)
Both ion and neutral forms in innter membrane.

8. Di-Aryl Amines as Non-Classical Uncouplers
Fluazinam - anti-fungal
Set 2447: log 1/C = 0.18 pKa – 1.57 bilin(pKa) log P’ ; n = 22; r2 = 0.96; OpKa = 6.96

9. McGowan volume and/or CMR may help explain the difference.
‘Normal’ π
Special’ π
#Expls
2-Cl
+0.72
-0.01 3
4-Cl
-0.02
3-CF3
+0.90
+0.01
2-F
+0.14
-0.07 1
2-Br
+0.87
-0.24 2
3-CH3
+0.51
-0.31
4-OCF3
+1.00
-0.18
In most cases another (Y) group also present, and so 'buttressing" effect possible.
McGowan volume and/or CMR may help explain the difference.

10. Classical Uncouplers (Protonophores)
2,4-DNP, 6-t-Bu
pKa 4.80; logP 3.55
Pentachlorophenol
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. Malonoben (SF-6847)
insecticide
Set 2257: 1/C = pKa P-F P-P NVE ; n = 39; r2 = 0.96

12. Uncouplers in Treatment of Obesity
R = CH3 = BHT
R = P+(Ph)3 = Mito-BHT (ant-obesity lead)
2,4-DNP (1930s)
Binds to adenine nucleotide translocase
Lowers membrane potential (ΔΨm)

13. Fenfluramine
N-Nitroso analog
metabolism
Mitochondrial toxicity: membrane swelling and release of Cyt-C.

14. Pharmaceuticals with UOP action
Amiodarone - anti-arrhythmic
Protonated logD ~ 5.0; inhibits complexes 1 & II
Kebuzone - anti-rheumatic

15. Complex I-II Inhibitors
Capsaicin Analogs
Set 6878: log 1/C = 3.44 CLOGP – 0.28 (CLOGP)2 – n = 6; r2 = 0.98; OLP = 6.08

16. Complex I-II Inhibitors
Rotenone & Annonacin Analogs
Set 10754: Log 1/C = 0.14 CLOGP + 7.7; n = 5; r2 = 0.93

17. Complex I-II Inhibitors
4,7-subs. Acridones
Set 2373: Log 1/C = 0.74 CLOGP – 1.53 CLOGP2 – 1.36 σ ; n = 22; r2 = 0.90; OLP = 4.5

18. 2,3-alkyl-Quinolones
Set 3876: log P = 0.73 CLOGP – BiLinCLOGP I-3Me ; n = 12; r2 = 0.96; OLP = 5.65
Set 3877: Log 1/C = 0.67 CLOGP – 0.93 BiLin CLOGP I-Me ; n = 13; r2 = 0.86; OLP = 5.6

19. 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

20. Complex II-III Inhibition
Set 611: inhibition of succinate dehydrogenase in cinerea botrytis mold Log 1/C = 0.58 CLOGP NVE – 0.219; n = 21; r2 = .88
Set 699: acting as fungicide on rice sheath blight Log 1/C = MgVol MgVol ; n = 24; r2 = 0.88; Opt.vol. = 1.9

21. Complex II-III Inhibition
Set 1557: Benzanilides as fungicides inhibiting Complex II Log 1/C = 1.04 CLOGP – 1.7 Bilin CLOGP Es-X2 – B1-R σR ; n = 32; r2 = 0.89; OLP = 5.28

22. Complex II-III Inhibition
Set 1720: Thiazole-anilides as fungicides Log 1/C = 0.64 CLOGP σ I 2, ; n = 42; r2 = 0.85
I2,6 shows that di-ortho substitution is especially strong

23. Complex II-III Inhibition
Set 2425: Carboxins inhibiting Complex II of yeast pathogen c. laurentii Log 1/C = B1-4 – 0.72 σ – 1.32 I2, ; n = 14; r2 = 087
In this set, 2,6-disubstitution weakens inhibitory action.

24. 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 = σ ; n = 9; r2 = 0.97

25. Complex IV Inhibition
Set 3882: 4-quinolone analogs inhibiting bacterial cytochrome-C Log 1/C = 0.73 CLOGP – 0.83 bilinCLOGP 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 n = 21; r2 = 0.90; OLP = 6.35

26. anilino-thiadiazoles
Inhibitors of mammary sarcomas
Set 7095: C for maximal respiration release in rat liver mitochondria log 1/C = σ ; n = 5; r2 = 0.96
Set 7096: C for inhibition of ATP synthesis in rat liver mitochondria log 1/C = σ ; n = 6; r2 = 0.90

27. Mitochondrial Function
Protonophore: weak acid and hydrophobic (log P > 4)
Both ion and neutral forms in innter membrane.

28. Chloroplast ATP Production

29. Triazine inhibitors of Plastoquinone
Set 2252: Log 1/C = 0.61 log P bilinLogP WRB-X D-Y T1-Y -2.8 I-Me ; n = 47; r2 = 0.89; OLP = 4.5

30. Plastoquinone (atrazine target) in chloroplasts
Ubiquinone CoQ in mitochondria

31. Complex V Inhibition
Set 8510: Salicylanilides on exchange of P with ATP in fly mitochondria Log 1/C = NVE ; n = 15; r2 = 0.95

32. 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 ; n = 12; r2 = 0.95

33. Anilino-Thiadiazoles
Set 116: Rat liver mitochondria; 2-X-anilino-1,3,4- thiadiazoles; uncoupling oxidative phosphorylation Log 1/C = 1.01 I(CF3) σ ; 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) σ ; n = 13; r2 = 0.9

34. Uncouplers in Both Mitochondria & Chloroplasts
Pendimethalin (UOP measured; contradicts 1999 EPA manual)
Trifluralin (UOP measured in plant mitochondria)
Oryzalin
(probable)

35. Measurement of Proton Gradient (ΔΨm)
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?

36. 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.

39. 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.