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.

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.

Precursors of Chloroplasts & Mitochondria

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

Mitochondria

Chloroplasts

Mitochondrial Function

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

Fluazinam - anti-fungalFluazinam - 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

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-Bu2,4-DNP, 6-t-BupKa 4.80; logP 3.55pKa 4.80; logP 3.55

PentachlorophenolPentachlorophenolpKa 4.69; logP 5.12pKa 4.69; logP 5.12

• Set 599: I-50 respiration, rat liver mitochondriaLog 1/C = 1.73 CLOGP – 1.51 bilinCLOGP -0.51;n = 21; r2 = 0.89; OLP =~5.6

• 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 = CHR = CH33 = BHT = BHTR = PR = P++(Ph)(Ph)33 = Mito-BHT (ant- = Mito-BHT (ant-obesity lead)obesity lead)

•Binds to adenine nucleotide translocase

• Lowers membrane potential (ΔΨm)

Uncouplers in Treatment of Obesity

2,4-DNP (1930s)2,4-DNP (1930s)

• Mitochondrial toxicity: membrane swelling and release of Cyt-C.

FenfluramineFenfluramine

N-Nitroso analogN-Nitroso analog

metabolism

Pharmaceuticals with UOP action

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

Kebuzone - anti-rheumaticKebuzone - anti-rheumatic

Capsaicin AnalogsCapsaicin Analogs

Complex I-II Inhibitors

• Set 6878:log 1/C = 3.44 CLOGP – 0.28 (CLOGP)2 – 4.67n = 6; r2 = 0.98; OLP = 6.08

Rotenone & Annonacin AnalogsRotenone & Annonacin Analogs

Complex I-II Inhibitors

• Set 10754:Log 1/C = 0.14 CLOGP + 7.7; n = 5; r2 = 0.93

4,7-subs. Acridones4,7-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

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

• Set 699: acting as fungicide on rice sheath blightLog 1/C = -19.9 MgVol + 5.3 MgVol2 + 21.7; n = 24; r2 = 0.88;Opt.vol. = 1.9

Complex II-III Inhibition

• Set 1557: Benzanilides as fungicides inhibiting Complex IILog 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 fungicidesLog 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

Complex II-III Inhibition

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

Complex IV Inhibition

• Set 3882: 4-quinolone analogs inhibiting bacterial cytochrome-CLog 1/C = 0.73 CLOGP – 0.83 bilinCLOGP + 0.53n = 12; r2 = 0.95; OLP = 5.86

• Set 4985: Very similar relationships with cytochrome-C from beef heart mitochondriaLog 1/C = 0.86 CLOGP – 1.29 bilinCLOGP + 2.82n = 21; r2 = 0.90; OLP = 6.35

• Set 7095: C for maximal respiration release in rat liver mitochondrialog 1/C = -1.33 σ - + 9.71; n = 5; r2 = 0.96

• Set 7096: C for inhibition of ATP synthesis in rat liver mitochondrialog 1/C = -1.26 σ -- + 9.56; n = 6; r2 = 0.90

anilino-thiadiazolesInhibitors of mammary sarcomas

Mitochondrial Function

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

Chloroplast ATP Production

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

Complex V Inhibition

• Set 8510: Salicylanilides on exchange of P with ATP in fly mitochondriaLog 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 mitochondriaLog 1/C = 1.91 σY = 0.54 L-X + 2.45; n = 12; r2 = 0.95

Anilino-Thiadiazoles

• Set 116: Rat liver mitochondria; 2-X-anilino-1,3,4-thiadiazoles; uncoupling oxidative phosphorylationLog 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-phosphorylationLog 1/C = 1.87 I(CF3) + 0.43 σ - + 3.5; n = 13; r2 = 0.9

Uncouplers in Both Mitochondria & Chloroplasts

PendimethalinPendimethalin(UOP measured; contradicts 1999 EPA manual)(UOP measured; contradicts 1999 EPA manual)

OryzalinOryzalin(probable)(probable)

TrifluralinTrifluralin(UOP measured in plant mitochondria)(UOP measured in plant mitochondria)

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?

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.

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.