Rhodoquinone mimetics and methods of making and using thereof

Abstract

Provided herein are rhodoquinone mimetics, including compounds defined by Formula I and Formula II. Also provided are methods, uses, and kits involving the disclosed compounds and pharmaceutical compositions thereof for treating and / or preventing a disease (e.g., a metabolic disorder (e.g., obesity, diabetes), a hypoxia related disease (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder), or a disease resulting from rhodoquinone depletion (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, or neurodegenerative disorder)) in a subject.

Description

Rhodoquinone Mimetics and Methods of Making and Using ThereofCROSS-REFERENCE TO RELATED APPLICATIONSThis application claims benefit of priority of U.S. Provisional Application No. 63 / 626,374, filed January 29, 2024, which is hereby incorporated by reference in its entirety.BACKGROUNDThe flow of electrons through the mitochondrial electron transport chain (ETC.) supports a diverse set of cellular processes, such as the synthesis of metabolites that support macromolecule production as well as the regulation of signaling and cell death pathways. Electrons enter the ETC through many routes, including from complex I and dihydroorotate dehydrogenase (DHODH), move between complexes via an electron carrier, and exit by reducing a terminal electron acceptor. Ubiquinone (UQ), the only known electron carrier in the mammalian ETC, delivers electrons to both oxygen (O2) and fumarate as terminal electron acceptors. As fumarate has a lower reduction potential than UQ, fumarate reduction is only thermodynamically favorable when ubiquinol, the reduced form of UQ, accumulates. Paradoxically, some tissues reduce fumarate without ubiquinol buildup, suggesting another mechanism enables fumarate reduction in mammals. However, to date, such alternative mechanisms remain largely unexplored. Uncovering the details of these pathways can provide opportunities to develop new therapeutic strategies to treat a variety of diseases and disorders.SUMMARYProvided herein are compounds (rhodoquinone mimetics) defined by Formula I or Formula II belowor a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from, Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; R1is chosen from Ci-Ce alkyl and Ci-Ce haloalkyl; R2and R2are independently chosen from hydrogen, C i -Ce alkyl, and C i -Ce haloalkyl, or R2and R2, together with the nitrogen atom to which they are attached, combine to form a 3 to 7 membered heterocycloalkyl ring; R3is chosen from hydrogen, Ci-Ce alkyl, and Ci-Ce haloalkyl; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkyl thio, C1-6 alkylsulfinyl, Ci- 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(C 1-6 alky l)carbamyl, carboxy, C1-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, Ci-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, Ci .6 alkylaminosulfonylamino, di(Ci-6 alkyl)aminosulfonylamino, aminocarbonylamino, Ci-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.In some embodiments of Formula I and Formula II, R1can be methyl. In some embodiments of Formula I and Formula II, R1can be CF3. In some embodiments of Formula I and Formula II, R2and R2can be hydrogen. In some embodiments of Formula I and Formula II, R3can be methyl.In some embodiments of Formula I and Formula II, R3can be CF3.In some embodiments of Formula I and Formula II, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula I and Formula II, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, C - 12 alkyl, or Cs-16 alkyl). In certain embodiments of Formula I and Formula II, Z is Ce-24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-i8 heteroalkyl, Ce-i2 heteroalkyl, or Cs ie heteroalkyl). In some embodiments of Formula I and Formula II, Z can be Ce-24 alkyl, optionally substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by a hydroxy group). In some embodiments of Formula I and Formula II, Z can be Ce-24 alkylaryl, optionally substituted by 1, 2, or 3 independently selected RAgroups.In other embodiments of Formula I and Formula II, Z is. In some of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula I and Formula II, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula I and Formula II, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula I and Formula II where Z is / x L / Athe mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can be defined by Formula IA or Formula IIA belowor a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from / x L / A, Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, CM haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkylthio, C1-6 alkylsulfinyl, Ci- 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(Ci-6alkyl)carbamyl, carboxy, C1-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, CM alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(C alkyl)aminosulfonyl, aminosulfonylamino, Ci -6 alkylaminosulfonylamino, di(Ci-6 alkyl)aminosulfonylamino, aminocarbonylamino, C alkylaminocarbonylamino, and di(Ci e alkyl)aminocarbonylamino.In some embodiments of Formula IA and Formula IIA, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IA and Formula IIA, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-i2 alkyl, or Cs-ie alkyl). In certain embodiments of Formula IA and Formula IIA, Z is Ce- 24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-is heteroalkyl, Ce-12 heteroalkyl, or Cs-ie heteroalkyl). In certain embodiments of Formula IA and Formula IIA, Z can be Ce-24 alkyl, optionally substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by a hydroxy group). In certain embodiments of Formula IA and Formula IIA, Z can be Ce-24 alkylaryl, optionally substituted by 1, 2, or 3 independently selected RAgroups.In other embodiments of Formula IA and Formula IIA, Z is. In some of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula IA and Formula IIA, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IA and Formula IIA, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula IA and Formula IIA where Z is, the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can be defined by Formula IB or Formula IIB belowFormula IB Formula IIB or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from, Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkylthio, C 1-6 alkylsulfinyl, Ci- 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(Ci-6 alkyl)carbamyl, carboxy, C1-6 alkylcarbonyl, C1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, C1-6 alkylaminosulfonylamino, di(C 1-6 alky l)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.In some embodiments of Formula IB and Formula IIB, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IB and Formula IIB, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-i2 alkyl, or Cs-ie alkyl). In certain embodiments of Formula IB and Formula IIB, Z is Ce- 24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-is heteroalkyl, Ce-i2 heteroalkyl, or Cs-ie heteroalkyl). In certain embodiments of Formula IB and Formula IIB, Z can be Ce-24 alkyl, optionally substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by a hydroxy group). In certain embodiments of Formula IB and Formula IIB, Z can be Ce-24 alkylaryl, optionally substituted by 1, 2, or 3 independently selected RAgroups.In other embodiments of Formula IB and Formula IIB, Z is. jnsome of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula IB and Formula IIB, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IB and Formula IIB, L represents a C3-18 heteroalkylene group optionally substituted by 1 , 2, or 3 independently selected RAgroups.In some embodiments of Formula IB and Formula IIB where Z is, the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cationor a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can be defined by Formula IC or Formula IIC belowFormula IC Formula IIC or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from, Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkylthio, C1-6 alkylsulfinyl, Ci- 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(Ci-6 alkyl)carbamyl, carboxy, C1-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, Ci -6 alkylaminosulfonylamino, di(C 1-6 alky l)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.In some embodiments of Formula IC and Formula IIC, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IC and Formula IIC, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-i2 alkyl, or Cs-ie alkyl). In certain embodiments of Formula IC and Formula IIC, Z is Ce- 24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-is heteroalkyl, Ce-12 heteroalkyl, or Cs-ieheteroalkyl). In certain embodiments of Formula IC and Formula IIC, Z can be Ce-24 alkyl, optionally substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by a hydroxy group). In certain embodiments of Formula IC and Formula IIC, Z can be Ce-24 alkylaryl, optionally substituted by 1, 2, or 3 independently selected RAgroups.In other embodiments of Formula IC and Formula IIC, Z is. lnsome of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula IC and Formula IIC, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IC and Formula IIC, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula IC and Formula IIC where Z is .L / A, the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can comprise one of the following:wherein n is an integer from 3 to 18, Ph represents phenyl, and TPP represents a triphenylphosphonium cation.Also provided herein are kits and pharmaceutical compositions comprising therapeutically effective amount of a compound (rhodoquinone mimetic) described herein. In some embodiments, the therapeutically effective amount of the compound can be encapsulated in delivery vehicle, such as a liposome, lipid nanoparticle, or polymeric nanoparticle.Also provided herein are methods of treating a disease in a subject in need thereof using the compounds (rhodoquinone mimetics) described herein. For example, provided herein are methods of treating a disease in a subject in need thereof that comprise administering to the subject a therapeutically effective amount of a compound (rhodoquinone mimetic) described herein. In some embodiments, the disease can be a mitochondrial disorder, a metabolic disorder (e.g., obesity, diabetes), a disorder that induces or results from oxidative stress, an oxygen free radical disorder including a hypoxia related disease, inflammation, or a disease resulting from rhodoquinone depletion.In some embodiments, the disease can comprise a hypoxia related disease, i.e., where the body or any region of the body has been deprived of adequate oxygen supply (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder).In certain embodiments, the disease can comprise ischemia (e.g., ischemia of the pancreas, adipose tissue, skeletal muscle, brain, kidney, liver, gastrointestinal tract, heart, or lung).In certain embodiments, the disease can comprise hypoxia (e.g., exercise-induced hypoxia, hypoxia resulting from ischemia, hypoxia of the heart, and / or hypoxia of the lung).In some embodiments, the disease can comprise a disease resulting from rhodoquinone depletion (e.g., a proliferative disease (e.g., cancer), inflammatory disease, neuromuscular disorder (e.g., a mitochondrial myopathy), metabolic disorder, or neurodegenerative disorder (e.g., a disorder that results from mutations in the mitochondrial DNA).In certain emboidments, the disease can comprise CoQ-10 deficiency.In certain emboidments, the disease can comprise a mitochondrial complexIII deficiency.In certain emboidments, the disease can comprise a mitochondrial complexIV deficiency.In certain embodiments, methods of treating disease can further comprise administering an additional active agent to the subject. In certain embodiments, the additional active agent can be chosen from a vitamin, an antioxidant, an antiinflammatory, an anti-cancer agent, an anti-obesity agent, a probiotic, an antibiotic, a statin, or a plasmid (e.g., a plasmid encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., RquA))), or a combination thereof.Also provided herein are methods of reducing oxidation and / or oxidative stress in a biological sample that comprise contacting the biological sample with a compound (rhodoquinone mimetic) described herein.Also provided herein are methods for reducing or preventing oxidation in a composition that comprise contacting the composition with a compound (rhodoquinone mimetic) described herein. In certain embodiments, the composition can comprise a food, a nutrient, a chemical, a pharmaceutical agent, a polymer, a biological sample, a protein, or a nucleic acid.Also provided herein are methods of using the compounds (rhodoquinone mimetics) described herein as antioxidants or preservatives, as nutritional supplements, and ex vivo to prevent oxidative and / or oxidative stress in a biological sample, such as blood, tissue, and / organs in storage and / or blood, tissue, and / organs before and / or during transplantation.DESCRIPTION OF DRAWINGSFigures 1A-1K. Rhodoquinone is a component of mammalian mitochondria. Figure 1A. Rates of fumarate reduction and succinate oxidation in mitochondria from mouse kidney and brain. Fumarate reduction was initiated with 10 mM fumarate and 10 mM NADH + / - 5 mM malonic acid. Succinate oxidation reaction was initiated with 10 mM succinate + / - 5 mM malonic acid. Data represent mean + / - SEM, n = 4 biological replicates. Figure IB. Ubiquinone-9 : ubiquinol-9 in mouse tissues. Data represent the mean + / - SEM, n=5 female C57 BL / 6 mice age 10 weeks. Figure 1C. Ubiquinone-9 and rhodoquinone-9 and their standard reduction potentials (E’o). Figures 1D-1E. Chromatograms and fragmentation of ubiquinone-9 and rhodoquinone-9 in mouse kidney and C. elegans. Figure IF. Absolute quantification of rhodoquinone-9 in mitochondria from mouse tissues. Data represent the mean + / - SEM, n=6 male C57 BL / 6 mice age 10 weeks. Figures 1G-1H. Ubiquinone-9 and rhodoquinone-9 in 20 qg of whole tissue lysates and mitochondria. Datarepresent the mean + / - SEM, n=6 male C57 BL / 6 mice age 10 weeks. P values calculated using a parametric t test. Figure II. Ratio of the total rhodoquinone-10 : ubiquinone- 10 in mitochondria from human kidney, brain, and muscle, and rhodoquinone-9 : ubiquinone-9 in C. elegans. Data represent the mean + / - SEM, n=5. Figures 1J-1K. Relative ubiquinone-10 and rhodoquinone-10 in 20 qg of whole tissue lysates and mitochondria. Data represent the mean + / - SEM, n=5. P values calculated using a parametric t test. For all panels, ns indicates not significant, *P < 0.05, **P < 0.01, ***P < 0.001, **** P < 0.0001. See also Figures 7A-7L and Figures 8A-8Q.Figures 2A-2H. Rhodoquinone carries electrons to fumarate as the terminal electron acceptor. Figure 2A. Schematic of ETC pathways. Figure 2B. RquA reaction and LC-MS detection of rhodoquinone-10 synthesis in 143B cells. Figure 2C. Rhodoquinone-10: ubiquinone-10 in 143B cells treated with a dose of doxycycline. Data represent the mean + / - SEM, n=3. Figures 2D-2E. Schematics of13Cs-glutamine tracing and13C4-aspartate tracing to measure the forward and reverse activities of SDH. Red indicates the13C isotope. Figure 2F. Fumarate reduction and succinate oxidation using 2 mM13C5l 5N2-glutamine tracing for 8 hours in wild-type and RquA-expressing 143B cells + / - 500 nM Antimycin. Data represent the mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 2G. Fumarate reduction using 10 mM13C4-aspartate tracing for 8 hours in wild-type, RquA- expressing, and RquA-expressing SDHB knockout 143B cells. Data represent the mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 2H. Fumarate reduction in mitochondria from wild-type and RquA-expressing 143B cells. Data represent mean + / - SEM, n = 4 replicates fitted using nonlinear regression. P value calculated using a parametric t test on the final timepoint. For all panels, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. See also Figures 9A-9R and Figures 10A-10K.Figures 3A-3G. Rhodoquinone analogs drive fumarate reduction. Figure 3A. HKJS-001 and HKJS-003. Figures 3B-3C. Fumarate reduction using 2 mM13Cs15N2- glutamine tracing for 8 hours in wild- type and SDHB knockout 143B cells treated 10 qM HKJS-001 or 100 nM HKJS-003. Data represent the mean + / - SEM, n=3. Figure 3D. Workflow for SDH activity assay on purified mitochondria. Figure 3E-3G. Fumarate reduction in purified mitochondria from wild- type and SDHB knockout 143B cells with either DMSO, 10 / J.M HKJS-001 or 100 nM HKJS-003. Data represent mean + / - SEM, n = 4 replicates fitted using a nonlinear regression. P value calculated using a parametric t teston the final timepoint. For all panels, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. See also Figures 11A-11N and Figures 12A-12F.Figures 4A-4L Ubiquinone and Rhodoquinone support distinct repertoires of mitochondrial function. Figure 4A. Volcano plot depicting metabolite profiling of wildtype and RquA-expressing 143B and Caki-1 cells, n = 3 biological replicates per condition. P values calculated using a parametric t test. Figure 4B. Mitochondrial membrane potential in wild-type and RquA-expressing 143B and Caki-1 cells. 500 nM Carbonyl cyanide m- chlorophenyl hydrazone (CCCP) was added 30 minutes prior to staining. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 4C. ATP : ADP ratio in wild-type, RquA-expressing, and RquA-expressing SDHB knockout 143B cells. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 4D. Proliferation of wild-type, RquA-expressing, and RquA-expressing SDHB knockout 143B cells in media containing glucose or galactose for 5 days. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 4E. DHODH activity using stable isotope tracing of 10 mM13C4-aspartate for 6 hours in wild-type and RquA- expressing 143B cells + / - 5 qM Brequinar. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 4F. Reduced (GSH) to oxidized (GSSG) ratio in wild-type, RquA-expressing, and RquA-expressing SDHB knockout 143B cells. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 4G. Hydrogen peroxide (H2O2) in wild-type and RquA-expressing 143B and Caki-1 cells. 100 qM Tert-butyl hydroperoxide and 1.25 mM N-acetyl cysteine were added 30 minutes prior to analysis. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figure 4H. Superoxide measured by LC-MS analysis of 2-OH Mitoethidium upon Mitosox treatment in wild-type and RquA-expressing 143B and Caki-1 cells. Data represent mean + / - SEM, n=3. P values calculated using a parametric t test. Figure 41. Schematic depicting mitochondrial functions supported by ubiquinone and rhodoquinone. For all panels, ns indicates not significant, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. See also Figures 13A-13H and Figures 14A-14O.Figures 5A-5J. Reprogramming the ETC mitigates metabolic stress upon hypoxia. Figure 5A. Schematic of UQ and RQ-directed ETCs in hypoxia. Figure 5B. Immunoblot analyses of wild-type and RquA-expressing Caki-1 cells in normoxia or 0.5% O2 for 6 days. Figure 5C. Log2 fold change of RNA seq units from wild-type or RquA-expressing cellscultured in in normoxia or 0.5% O2 for 7 days. P values calculated using a parametric t test. Figures 5D-5E. LC-MS analysis of glucose and lactate in the media of wild-type and RquA-expressing 143B cells cultured in normoxia or 0.5% O2 for 6 days. Analysis also performed on wild-type 143B cells + / - 10 / zM HKJS-001. Data represent mean + / - SEM, n=3. P values calculated using a parametric t test. Figure 5F. Reduced (GSH) to oxidized (GSSG) ratio in wild-type and RquA-expressing Caki-1 cells cultured in normoxia or 0.5% O2 for 6 days. Data represent mean + / - SEM, n=3. P values calculated using a one-way ANOVA. Figures 5G-5H. Superoxide measured by LC-MS analysis of 2-OH Mitoethidium upon Mitosox treatment in wild-type and RquA-expressing 143B cells cultured in normoxia or 0.5% O2 for 6 days. Analysis also performed on wild-type 143B cells + / - 10 zM HKJS- 001. Data represent mean + / - SEM, n=3. P values calculated using a parametric t test. Figures 5I-5J. H O2 in wild-type and RquA-expressing Caki-1 cells cultured in normoxia or 0.5% O2 for 6 days. Analysis also performed on wild-type 143B cells + / - 10 / zM HKJS- 001. Data represent mean + / - SEM, n=3. P values calculated using a parametric t test. For all panels, ns indicates not significant, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. See also Figures 15A-15I and Figures 16A-16G.Figures 6A-6J. Reprogramming the ETC mitigates ischemia reperfusion injury. Figure 6A. Schematic of13Cs15N2-glutamine tracing in vivo. Figure 6B. Rhodoquinone-9 : ubiquinone-9 in 20 / zg of mitochondria from livers infected with AAV-mCherry or AAV- RquA for 7 days. Data represent the mean + / - SEM, n=8 mCherry and n=6 RquA male C57 BL / 6 mice age 8 weeks. P values calculated using a parametric t test. Figure 6C. Absolute quantification of13Cs-citrate,13C3-malate,13C3-fumarate, and13C3-succinate in AAV9- mCherry or AAV9-RquA livers. Data represent the mean + / - SEM, n=8 mCherry and n=6 RquA male C57 BL / 6 mice age 8 weeks. P values calculated using a parametric t test. Figure 6D. Reduced (GSH) : oxidized (GSSG) glutathione in AAV9-mCherry or AAV9- RquA livers. Data represent the mean + / - SEM, n=5 mCherry and n=8 RquA male C57 BL / 6 mice age 10 weeks. Figure 6E. ATP : ADP in AAV9-mCherry or AAV9-RquA livers. Data represent the mean + / - SEM, n=5 mCherry and n=8 RquA male C57 BL / 6 mice age 10 weeks. Figure 6F. Metabolomics of mouse liver after injection of13Cs15N2- glutamine + / - 6.5 mg / kg HKJS-001 + / - 160 mg / kg malonic acid. Absolute quantification of13C3-succinate and13C3-fumarate. Data represent the mean + / - SEM, n=5 male C57 BL / 6 mice age 12 weeks. P values calculated using a one-way ANOVA. Figure 6G. Schematicof ischemia study. Figure 6H. Reduced (GSH) : oxidized (GSSG) glutathione 2 and 24 hours after induction of ischemia in mice pretreated + / - 6.5 mg / kg HKJS-001. Data represent the mean + / - SEM, n=4 male C57 BL / 6 mice age 14 weeks. Figures 6I-6J. Laser doppler imaging and quantification on the day of surgery (day 0) and during recovery (3 and 7 days) after induction of ischemia. Data represent the mean + / - SEM, n=5 male C57 BL / 6 mice age 12 weeks. For all panels, ns indicates not significant, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. See also Figures 17A-17N.Figures 7A-7L. Rhodoquinone is a novel component of mammalian mitochondria, Related to Figures 1A-1K. Figure 7A. Schematic of in vivo13Cs15N2-glutamine tracing workflow to measure fumarate reduction. Figure 7B. Ratio of fumarate reduction to succinate oxidation in mouse tissues after injection of13C515N2-glutamine. Absolute quantification of13C3-fumarate,13C4-fumarate,13C3-succinate, and13C4-succinate was performed. Fumarate reduction was calculated as the pmoles / gg13C3-succinate / 3Cs- fumarate. Succinate oxidation was calculated as the pmoles / gg13C4-fumarate / 13C4- succinate. Data represent the mean + / - SEM, n=4 wild-type male C57 BL / 6 mice 12 weeks old. Figure 7C. Pearson correlation analysis of data the ubiquinone:ubiquinol ratio against the relative levels of fumarate reduction (FR) over succinate oxidation (SO). Each dot represents the average of each value in a given tissue. Figure 7D. Relative rhodoquinone in 20 gg worth of mitochondria purified from mouse tissues. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 7E. Relative rhodoquinol in 20 gg worth of mitochondria purified from mouse tissues. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 7F. Total ubiquinone is the sum of the ion counts of the oxidized (ubiquinone-9) and reduced (ubiquinol-9) forms. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 7G. Relative ubiquinol in 20 gg worth of mitochondria purified from mouse tissues. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 7H. Relative ubiquinone in 20 gg worth of mitochondria purified from mouse tissues. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 71. Relative rhodoquinone-9 and rhodoquinol-9 in 20 gg of mitochondria purified from mouse tissues. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 7J. Ratio of the total ion counts of rhodoquinone and ubiquinone in mitochondria purified from mouse tissues. Totalubiquinone is the sum of the ion counts of the oxidized (ubiquinone-9) and reduced (ubiquinol-9) forms. Total rhodoquinone is the sum of the ion counts of the oxidized (rhodoquinone-9) and reduced (rhodoquinol-9) forms. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. Figure 7K. Extracted ion chromatogram (EIC) and fragmentation pattern of a crude rhodoquinone-9 standard purified from Ascaris suum. Figure 7L. Standard curve of rhodoquinone-9 standard. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 8A-8Q. UQ and RQ enrichment in mitochondria from mouse tissues. Figures 8A-8F. Relative ubiquinone-9 and rhodoquinone-9 in 20 g worth of protein material in whole tissue lysates and purified mitochondria. Data represent the mean + / - SEM, n=6 wild-type male C57 BL / 6 mice age 10 weeks old. P values were calculated using a parametric t test in graphpad prism. Figure 8G. Analysis of isoprene tail lengths of quinone species in mice. Extracted ion chromatogram (EIC) of the proton adduct of ubiquinone, rhodoquinone, and menaquinone with 1-10 isoprene unit tails in mitochondria purified from mouse kidney. Figures 8H-8Q. Fragmentation of Rhodoquinone-9 and Rhodoquinol-9 in mouse tissues. The fragmentation products of rhodoquinone-9 and rhodoquinol-9 peaks detected by LC-MS analysis of mitochondria purified from mouse tissues. The fragmentation was performed on the mass depicted representing the proton adducts of rhodoquinone-9 and rhodoquinol-9 ionized in positive ion mode and at the retention times of ~5.3 minutes and ~4.8 minutes, respectively. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 9A-9R. Rhodoquinone is detected in human tissues but not in cell lines of tissue origin, Relative to Figures 2A-2H. Figure 9A. Extracted ion chromatogram (EIC) and fragmentation pattern of a crude rhodoquinone- 10 standard purified from Rhodospirillum rubrum. Figure 9B. Relative ubiquinone-10 and rhodoquinone- 10 in 20 pg worth of protein material in whole tissue lysates and purified mitochondria from post mortem human muscle. Data represent the mean + / - SEM, n=5 tissue samples. P values were calculated using a parametric t test in graphpad prism. Figures 9C-9J. Ion counts of ubiquinone-10 and rhodoquinone- 10 upon LC-MS analysis of a panel of cell lines cultured in normoxia and 0.5% O2 for 4 days. Data represent the mean + / - SEM, n=3 replicates percondition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 9K. Total ubiquinone and rhodoquinone in liver tissue and primary hepatocytes isolated from this tissue. Total ubiquinone is the sum of the ion counts of the oxidized (ubiquinone- 9) and reduced (ubiquinol-9) forms. Total rhodoquinone is the sum of the ion counts of the oxidized (rhodoquinone-9) and reduced (rhodoquinol-9) forms. Data represent the mean + / - SEM, n=6 replicates of cultured hepatocytes. P values were calculated using a one-way ANOVA in graphpad prism. Figures 9L-9M. Immunoblot analyses of FLAG, Actin, and TOMM20 in 143B and Caki-1 RquA cells treated with a dose of doxycycline for 72 hours. Figure 9N. Immunofluorescence analysis of FLAG and C0X4 in 143B RquA cells treated with 100 ng / mL doxycycline for 48 hours. Figure 90. Blue native PAGE gel depicting in tact ETC complexes I-V from mitochondria purified from 143B wild-type and RquA- expressing cells treated with 250 ng / mL doxycycline for 48 hours. Figure 9P. Immunoblot analyses of FLAG, ATP5A and, UQCRC2 in mitochondria purified from 143B wild-type and RquA-expressing cells treated with 250 ng / mL doxycycline for 48 hours. Figure 9Q. The relative ion counts of rhodoquinone- 10 and ubiquinone- 10 in wild-type and RquA- expressing 143B cells treated with a dose of doxycycline as measured by LC-MS. Data represent the mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 9R. Oxygen consumption rate in wild-type and RquA- expressing 143B cells treated with a dose of doxycycline for 48 hours. 500 nM Antimycin A was injected at the designated timepoint. Data represent the mean + / - SEM, n=3 per condition. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001 , and **** indicates P < 0.0001.Figures 10A-10K. RquA expression drives fumarate reduction in normoxia, Related to Figures 2A-2H. Figures 10A-10B. Fumarate reduction and succinate oxidation as determined using stable isotope tracing of 2 mM13C515N2-glutamine for 8 hours and LC- MS analysis. Tracing was performed in wild-type and RquA-expressing DLD1 and HCT116 cells treated with 250 ng / mL doxycycline and either vehicle or 500 nM Antimycin A. Data represent the mean + / - SEM, n=3 biological replicates per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 10C. The ratio of rhodoquinone- 10 and ubiquinone-10 (left), the ratio of ubiquinone-10 : ubiquinol-10 (middle), and the ratio of rhodoquinone- 10 : rhodoquinol-10 in wild-type and RquA- expressing 143B cells treated with 250 ng / mL doxycycline and exposed to hypoxia for 72 hours. Data represent the mean + / - SEM, n=3 per condition. P values were calculated usinga one-way ANOVA in graphpad prism. Figure 10D. Immunoblot analyses of FLAG, Actin, and SDHB in 143B wild-type, RquA-expressing, and RquA-expressing SDHB knockout cells treated with 250 ng / mL doxycycline for 72 hours. Figures 10E-10F. Fumarate reduction and succinate oxidation as determined using stable isotope tracing of 2 mM13Cs15N2-glutamine for 8 hours and LC-MS analysis. Tracing was performed in wildtype, RquA-expressing, and RquA-expressing SDHB knockout 143B cells. Data represent the mean + / - SEM, n=3 biological replicates per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 10G. Fumarate reduction and succinate oxidation as determined using stable isotope tracing of 2 mM13Cs15N2-glutamine for 8 hours and LC-MS analysis. Tracing was performed in wild-type and RquA-expressing 143B cells treated with or without 5 mM malonic acid. Data represent the mean + / - SEM, n=3 biological replicates per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 10H. Fumarate reduction as determined using stable isotope tracing of 10 mM13C4-aspartate for 8 hours and LC-MS analysis. Tracing was performed in wildtype, RquA-expressing, and RquA-expressing SDHB knockout 143B cells treated. Data represent the mean + / - SEM, n=3 biological replicates per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 101. Schematic of in vitro fumarate reduction assay performed on mitochondria purified from wild-type and RquA- expressing 143B cells. Figure 10J. NAD+ and fumarate levels measured in the fumarate reduction assay performed on purified and permeabilized mitochondria from WT and RquA-expressing 143B cells. The reaction was initiated with 10 mM fumarate and 1 mM NADH and NAD+ production was monitored by LC-MS. Data represent mean + / - SEM, n = 4 biological replicates per time point. Data points were fitted using nonlinear regression. P value calculated using a parametric t test on the final timepoint. Figure 10K. Succinate oxidation measured in purified and permeabilized mitochondria from WT and RquA- expressing 143B cells. The reaction was initiated with 10 mM succinate and monitored through the production of fumarate over time by LC-MS. Data represent mean + / - SEM, n = 4 biological replicates per time point. Data points were fitted using nonlinear regression. P value calculated using a parametric t test on the final timepoint. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 11A-11N. The impact of HKJS-001 and HKJS-003 on ubiquinone and respiration levels, Related to Figures 3A-3G. Figures 11A-11E. NMR analysis of the RQanalogs HKJS-001 and HKJS-003. Figure 11F. Ubiquinone- 10, rhodoquinone-10, HKJS- 001, and HKJS-003 docking conformation in Complex I (RCSB Protein Data Bank (PDB): 5XTD) and highlighting ligand interactions with residues Tyr108in NDUFS2, colored in orange, and His92in NDUFS2, colored in green. Figure 11G. Ubiquinol-10, Rhodoquinol- 10, HKJS-001, and HKJS-003 docking conformation in Complex II (RCSB Protein Data Bank (PDB): 8GS8) and highlighting ligand interactions with residues: Tyr114in SDHD colored in green, Trp201in SDHB, colored in pink, Trp61in SDHC, colored in yellow, and Met65in SDHC, colored in orange. Both complex I and II structures were prepared for docking by first removing water molecules and ligands. Polar hydrogens were added using AutoDockTools (Version 1.5.7). Ligand structures were prepared using Avogadro (Version 1.2). Docking search spaces were defined using PyRx (Version 0.8). Docking visualizations were generated using PyMol (Version 3.0.3, Schrodinger, LLC.). Molecular docking and free energy calculations were performed using AutoDock Vina (Version 1.1.2). Figures 11H-11L The relative ion counts of ubiquinone-10 as measured by LC-MS in wild-type 143B cells treated with either vehicle or 10 / zM HKJS-001 or 100 nM HKJS-003 for 48 hours. Data represent the mean + / - SEM, n=3 per condition. P values were calculated using a using a parametric t test in graphpad prism. Figures 11J-11N. Oxygen consumption rate in wild-type, RquA-expressing 143B cells, and 143B cells treated with either DMSO, 10 / zM HKJS-001 or 100 nM HKJS-003 for 24 hours. The mitochondrial stress test was performed with 2 qM Oligomycin, 2 qM FCCP, and 1 qM Antimycin and Rotenone. Calculations for Basal Respiration, Oi-linked ATP Production, Maximal Respiration, and Spare Respiratory Capacity were calculated based off the mitochondrial stress test in Figure S10C. Data represent the mean + / - SEM, n=5 per condition. P values were calculated using a one-way ANOVA in graphpad prism. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 12A-12F. HKJS-001 and HKJS-003 drive fumarate reduction in normoxia, Related to Figures 3A-3G. Figures 12A-12B. Succinate oxidation as determined using stable isotope tracing of 2 mM13Cs15N2-glutamine for 8 hours and LC-MS analysis in wildtype 143B cells. Cells were treated with either vehicle or 10 / zM HKJS-001 or 100 nM HKJS-003. Data represent the mean + / - SEM, n=3 biological replicates per condition. P values were calculated using a parametric t test in graphpad prism. Figures 12C-12D.Fumarate reduction and succinate oxidation as determined using stable isotope tracing of 2 mM13Cs15N2-glutamine for 8 hours and LC-MS analysis. Tracing was performed in wildtype 143B cells treated with 100 nM CCCP or 100 nM HKJS-001. Data represent the mean + / - SEM, n=3 biological replicates per condition. P values were calculated using a one-way ANOVA calculated in graphpad prism. Figure 12E. Fumarate levels in the fumarate reduction reaction measured in purified and permeabilized mitochondria from wildtype and SDHB knockout 143B cells with either DMSO, 10 / zM HKJS-001 or 100 nM HKJS-003. The reaction was initiated with 10 mM fumarate and 10 mM NADH and monitored through the production of succinate over time by LC-MS. Data represent mean + / - SEM, n = 4 biological replicates per time point. Data points were fitted using a nonlinear regression. P value calculated using a parametric t test on the final timepoint. Figure 12F. NADH oxidation measured in the fumarate reduction assay performed on purified and permeabilized mitochondria from wildtype 143B cells treated with DMSO, 10 / zM HKJS- 001, or 100 nM HKJS-003. The reaction was initiated with 10 mM fumarate and 1 mM NADH and NAD+ production was monitored by LC-MS. Data represent mean + / - SEM, n = 4 biological replicates per time point. Data points were fitted using nonlinear regression. P value calculated using a parametric t test on the final timepoint. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 13A-13H. Ubiquinone and Rhodoquinone-directed ETC circuits support distinct repertoires of mitochondrial functions, Related to Figures 4A-4L Figure 13A. Metaboanalyst pathway analysis of the metabolic differences of wild-type and RquA- expressing Caki-1 cells. Figure 13B. The ratio of the ion counts of succinate and fumarate as measured by LC-MS analysis of wild-type and RquA-expressing 143B and Caki-1 cells treated with 250 ng / mL doxycycline for 72 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 13C. The ratio of the ion counts of ATP and ADP as measured by LC-MS analysis of wildtype and RquA-expressing 143B and Caki-1 cells treated with 250 ng / mL doxycycline for 72 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 13D. Proliferation of wild-type and RquA- expressing 143B and Caki-1 cells upon culturing in media containing glucose or galactose as the central carbon source for 5 days and treated with 250 ng / mL doxycycline. Datarepresent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 13E. The ratio of the ion counts of NAD+ and NADH as measured by LC-MS analysis of wild- type and RquA-expressing 143B and Caki-1 cells treated with 250 ng / mL doxycycline for 72 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 13F. Proliferation of wild-type, RquA-expressing, and RquA-expressing SDHB knockout 143B cells upon culturing in media containing either 1 mM pyruvate, no pyruvate, treated with either DMSO or 5 jitM Rotenone for 5 days in the presence of 250 ng / mL doxycycline. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA calculated in graphpad prism. Figure 13G. The relative levels of lactate as measured by LC-MS analysis of wild-type, RquA-expressing, and RquA-expressing SDHB knockout 143B cells treated with 250 ng / mL doxycycline for 72 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 13H. Proliferation of wild-type, RquA-expressing, and RquA-expressing SDHB knockout 143B cells upon culturing in media containing either 100 / zg / mL Uridine, no Uridine, treated with either DMSO or 5 / zM Brequinar for 6 days in 250 ng / mL doxycycline. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA in graphpad prism. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 14A-14O. The impacts of HKJS001 on mitochondrial functions, Related to Figures 4A-4L Figure 14A. Volcano plot depicting polar metabolite profiling of Caki-1 cells treated with either DMSO or 10 / zM HKJS-001 for 48 hours. n=3 biological replicates per condition. P values were calculated using a parametric t test. Figure 14B. Metaboanalyst pathway analysis of the metabolic differences of Caki-1 cells treated with either DMSO or 10 iM HKJS001 for 48 hours. Figure 14C. The ratio of the ion counts of succinate and fumarate as measured by LC-MS analysis of wild-type and SDHB knockout 143B cells treated with either DMSO or 10 / zM HKJS001 for 48 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 14D. Relative UTP levels as measured by LC-MS analysis of wild-type 143B cells treated with either DMSO or 10 / zM HKJS001 for 48 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpadprism. Figure 14E. DHODH activity as measured by stable isotope tracing of 10 mMnC4- aspartate for 6 hours in wild-type 143B cells treated with either DMSO or 10 / zM HKJS001 for 48 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 14F. Proliferation of wild-type 143B cells treated with either DMSO or 10 / zM HKJS001 and cultured in media containing either 100 / zg / mL Uridine, no Uridine, treated with either DMSO or 5 / zM Brequinar for 6 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 14G. The ratio of the ion counts of NAD+ and NADH as measured by LC-MS analysis of wild-type 143B cells treated with either DMSO or 10 / zM HKJS001 for 48 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 14H. Proliferation of wildtype 143B cells treated with either DMSO or 10 / zM HKJS001 and cultured in media containing either 1 mM pyruvate, no pyruvate, treated with either DMSO or 5 / zM Rotenone for 5 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 141. The ratio of the ion counts of ATP and ADP as measured by LC-MS analysis of wild-type 143B cells treated with either DMSO or 10 / zM HKJS001 for 48 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 14J. Proliferation of wild-type 143B cells cells treated with either DMSO or 10 / zM HKJS001 and cultured in media containing glucose or galactose as the central carbon source for 5 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 14K. The ratio of the ion counts of reduced (GSH) to oxidized (GSSG) glutathione as measured by LC-MS analysis of wild-type and RquA- expressing 143B and Caki-1 cells treated with 250 ng / mL doxycycline for 72 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figures 14L-14M. The ratio of the ion counts of reduced (GSH) and oxidized (GSSG) glutathione as measured by LC-MS analysis of wild-type and SDHB knockout 143B cells treated with either DMSO or 10 / zM HKJS001 or 100 nM HKJS003 for 48 hours. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 14N. Hydrogen peroxide (H2O2) levels in wild-type 143B treated with a dose of either HKJS-001 or N-acetyl cysteine for 48 hours. Analysis of CellRox Orange fluorescence by FACS. Data represent mean + / - SEM, n=3 percondition. Figure 140. Proliferation of RquA-expressing SDHB knockout 143B cells treated with 250 ng / mL doxycycline and cultured in either normoxia or 0.5% O2 for 8 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 15A-15I. Reprogramming the ETC promotes resistance to hypoxia exposure and oxidative stress in vivo, Related to Figures 5A-5J. Figure 15A. Gene set enrichment analysis of RNA sequencing data on wild-type and RquA-expressing 143B cells treated with 250 ng / mL doxycycline and cultured in either normoxia or 0.5% O2 for 6 days. Data plotted as log2 fold change of hypoxia / normoxia exposure in each cell line. Figure 15B. Principal component analysis of RNA sequencing results of wild-type and RquA- expressing 143B cells treated with 250 ng / mL doxycycline and cultured in either normoxia or 0.5% O2 for 6 days. Figure 15C. Comparative analysis of Hypoxia Gene Set Enrichment of wild-type versus RquA-expressing 143B cells cultured in normoxia and treated with 250 ng / mL doxycycline. P value calculated using FDR correction and correction for multiple testing. Figure 15D. Relative expression of representative genes in the Hypoxia Gene Set in wild-type versus RquA-expressing 143B cells in normoxia and hypoxia treated with 250 ng / mL doxycycline. P values were calculated using a one-way ANOVA test in graphpad prism. Figures 15E-15L Log2 fold change of RNA seq units from wild-type or RquA- expressing cells cultured in hypoxia (0.5% O2) or normoxia and treated with 250 ng / mL doxycycline. P values were calculated using a parametric t test in graphpad prism. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 16A-16G. Reprogramming the ETC mitigates hypoxia-induced proliferative and oxidative stress, Related to Figures 5A-5J. Figure 16A. Proliferation of wild-type and RquA-expressing 143B and Caki-1 cells treated with 250 ng / mL doxycycline and cultured in either normoxia or 0.5% O2 for 6 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figures 16B-16C. Proliferation of wild-type 143B treated with either DMSO or 10 / J.M HKJS001 or 100 nM HKJS003 and cultured in either normoxia or 0.5% O2 for 6 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test ingraphpad prism. Figure 16D. The ratio of the ion counts of reduced (GSH) to oxidized (GSSG) glutathione as measured by LC-MS analysis of wild-type 143B cells treated with either DMSO or 10 / rM HKJS001 and cultured in either normoxia or 0.5% O2 for 6 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA in graphpad prism. Figure 16E. Superoxide levels as measured by LC-MS analysis of 2-OH Mitoethidium, the oxidation product of Mitosox, in wild-type and RquA- expressing Caki-1 cells treated with 250 ng / mL doxycycline and cultured in either normoxia or 0.5% O2 for 6 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 16F. Hydrogen peroxide levels as measured by FACS analysis of CellRox Orange in wild-type and RquA-expressing 143B cells treated with 250 ng / mL doxycycline and cultured in either normoxia or 0.5% O2 for 6 days. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a parametric t test in graphpad prism. Figure 16G. Superoxide levels as measured by LC- MS analysis of 2-OH Mitoethidium, the oxidation product of Mitosox, after exposure to hypoxia (0.5% O2) for 0, 5, 10, 30, and 60 minutes in wild-type and RquA-expressing 143B cells treated with 500 ng / mL doxycycline 2 days prior to experimentation. Data represent mean + / - SEM, n=3 per condition. P values were calculated using a one-way ANOVA in graphpad prism. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figures 17A-17N. Reprogramming the ETC in vivo mitigates ischemic injury, Related to Figures 6A-6J. Figure 17A. Relative rhodoquinone and ubiquinone in 20 qg worth of mitochondria purified from livers infected with AAV-mCherry or AAV-RquA for 7 days. Data represent the mean + / - SEM, n=8 mCherry and n=6 RquA male C57 BL / 6 mice age 8 weeks old. P values were calculated using a parametric t test in graphpad prism. Figure 17B. Western blot analysis of livers infected with AAV-mCherry or AAV-RquA for 7 days. Figure 17C. Volcano plot depicting polar metabolite profiling of livers infected with AAV-mCherry or AAV-RquA for 7 days. n=8 mCherry and n=6 RquA male C57 BL / 6 mice age 8 weeks old. P values were calculated using a parametric t test. Figure 17D. Metaboanalyst pathway analysis of the metabolic differences of livers infected with AAV- mCherry or AAV-RquA for 7 days. Figure 17E. Schematic of workflow for in vivo tracing with the RQ analog HKJS-001. Figure 17F. LC-MS analysis of HKJS001 levels in the livers of wild-type male C57 BL / 6 mice age 12 weeks old treated with either vehicle or 6.5mg / kg HKJS001. Data represent mean + / - SEM, n=5 per condition. P values were calculated using a parametric t test in graphpad prism. Figures 17G-17H. Fraction labeling of13C3-fumarate and13Cs-succinate after injection of13Cs15N2-glutamine and either vehicle or 6.5 mg / kg HKJS001 with or without 160 mg / kg malonic acid. Data represent the mean + / - SEM, n=5 wild-type male C57 BL / 6 mice age 12 weeks old. P values were calculated using a parametric t test in graphpad prism. Figures 17I-17J. Metabolite analysis of mouse liver after injection of13Cs15N2-glutamine and either vehicle or 6.5 mg / kg HKJS001 with or without 160 mg / kg malonic acid. Absolute quantification of13C3-malate and13C5-citrate was performed. Data represent the mean + / - SEM, n=5 wild-type male C57 BL / 6 mice age 12 weeks old. P values were calculated using a one-way ANOVA in graphpad prism. Figures 17K-17L. The relative levels of reduced (GSH) and oxidized (GSSG) glutathione as measured by LC-MS analysis of healthy and ischemic muscle from mice pretreated with either vehicle or 6.5 mg / kg HKJS-001 and then subjected to hindlimb ischemia in one leg. Metabolites were extracted 2 and 24 hours post-induction of ischemia. Data represent the mean + / - SEM, n=4 wildtype male C57 BL / 6 mice age 14 weeks old. Figures 17M-17N. Quantification and images of of laser Doppler imaging to measure blood flow recovery 28 days after induction of hindlimb ischemia. Data represent the mean + / - SEM, n=5 wild-type male C57 BL / 6 mice age 12 weeks old per condition. For all data panels, ns indicates not significant, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001.Figure 18. Structure of rhodoquinone mimetics HKJS-011 to HKJS-020.DETAILED DESCRIPTION DefinitionsUnless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.The term “alkyl,” as used herein, refers to saturated straight, branched, cyclic, primary, secondary or tertiary hydrocarbons, including those having 1 to 20 atoms. In some embodiments, alkyl groups will include C1-C12, C1-C10, Ci-Cs, Ci-Ce, C1-C5, C1-C4, C1-C3, C1-C2, or Ci alkyl groups. Examples of C1-C10 alkyl groups include, but are not limited to, methyl, ethyl, propyl, 1 -methylethyl, butyl, 1 -methylpropyl, 2-methylpropyl, 1,1- dimethylethyl, pentyl, 1 -methylbutyl, 2-methylbutyl, 3-methylbutyl, 2,2-dimethylpropyl, 1- ethylpropyl, hexyl, 1 , 1 -dimethylpropyl, 1 ,2-dimethylpropyl, 1 -methylpentyl, 2- methylpentyl, 3-methylpentyl, 4-methylpentyl, 1 ,1 -dimethylbutyl, 1 ,2-dimethylbutyl, 1,3- dimethylbutyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl, 3,3-dimethylbutyl, 1-ethylbutyl, 2- ethylbutyl, 1 , 1 ,2-trimethylpropyl, 1,2,2-trimethylpropyl, 1 -ethyl- 1 -methylpropyl, l-ethyl-2- methylpropyl, heptyl, octyl, 2-ethylhexyl, nonyl and decyl groups, as well as their isomers. Examples of Ci-C4-alkyl groups include, for example, methyl, ethyl, propyl, 1 -methylethyl, butyl, 1 -methylpropyl, 2-methylpropyl and 1 ,1 -dimethylethyl groups.Cyclic alkyl groups or “cycloalkyl” groups, which are encompassed alkyl, include cycloalkyl groups having from 3 to 10 carbon atoms. Cycloalkyl groups can include a single ring, or multiple condensed rings. In some embodiments, cycloalkyl groups include C3-C4, C4-C7, C5-C7, C4-C6, or C5-C6 cyclic alkyl groups. Non-limiting examples of cycloalkyl groups include adamantyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl and the like.Alkyl groups can be unsubstituted or substituted with one or more moieties selected from the group consisting of alkyl, halo, haloalkyl, hydroxyl, carboxyl, acyl, acyloxy, amino, alkyl- or dialkylamino, amido, arylamino, alkoxy, aryloxy, nitro, cyano, azido, thiol, imino, sulfonic acid, sulfate, sulfonyl, sulfanyl, sulfinyl, sulfamonyl, ester, phosphonyl, phosphinyl, phosphoryl, phosphine, thioester, thioether, acid halide, anhydride, oxime, hydrazine, carbamate, phosphoric acid, phosphate, phosphonate, or any other viable functional group that does not inhibit the biological activity of the compounds of the invention, either unprotected, or protected as necessary, as known to those skilled in the art, for example, as described in Greene, et al., Protective Groups in Organic Synthesis, John Wiley and Sons, Third Edition, 1999, hereby incorporated by reference.Terms including the term “alkyl,” such as “alkylcycloalkyl,” “cycloalkylalkyl,” “alkylamino,” or “dialkylamino,” will be understood to comprise an alkyl group as defined above linked to another functional group, where the group is linked to the compound through the last group listed, as understood by those of skill in the art.The term “alkenyl,” as used herein, refers to both straight and branched carbon chains which have at least one carbon-carbon double bond. In some embodiments, alkenyl groups can include C2-C20 alkenyl groups. In other embodiments, alkenyl can include C2- C12, C2-C10, C2-C8, C2-C6 or C2-C4 alkenyl groups. In one embodiment of alkenyl, the number of double bonds is 1-3, in another embodiment of alkenyl, the number of double bonds is one or two. Other ranges of carbon-carbon double bonds and carbon numbers are also contemplated depending on the location of the alkenyl moiety on the molecule. “C2- Cio-alkenyl” groups may include more than one double bond in the chain. The one or more unsaturations within the alkenyl group may be located at any position(s) within the carbon chain as valence permits. In some embodiments, when the alkenyl group is covalently bound to one or more additional moieties, the carbon atom(s) in the alkenyl group that are covalently bound to the one or more additional moieties are not part of a carbon-carbon double bond within the alkenyl group. Examples of alkenyl groups include, but are not limited to, ethenyl, 1 -propenyl, 2-propenyl, 1-methyl-ethenyl, 1-butenyl, 2-butenyl, 3- butenyl, 1 -methyl- 1 -propenyl, 2-methyl-l -propenyl, l-methyl-2-propenyl, 2-methyl-2- propenyl; 1 -pentenyl, 2-pentenyl, 3-pentenyl, 4-pentenyl, 1 -methyl- 1 -butenyl, 2-methyl-l- butenyl, 3-methyl- 1-butenyl, l-methyl-2-butenyl, 2-methyl-2-butenyl, 3-methyl-2-butenyl,1-methyl-3-butenyl, 2-methyl-3-butenyl, 3-methyl-3-butenyl, l,l-dimethyl-2-propenyl, 1,2- dimethyl-1 -propenyl, 1 ,2-dimethyl-2-propenyl, 1 -ethyl- 1 -propenyl, l-ethyl-2-propenyl, 1- hexenyl, 2-hexenyl, 3-hexenyl, 4-hexenyl, 5-hexenyl, 1 -methyl- 1 -pentenyl, 2-methyl-l- pentenyl, 3 -methyl- 1 -pentenyl, 4-methyl-l -pentenyl, l-methyl-2-pentenyl, 2-methyl-2- pentenyl, 3-methyl-2-pentenyl, 4-methyl-2-pentenyl, l-methyl-3-pentenyl, 2-methyl-3- pentenyl, 3-methyl-3-pentenyl, 4-methyl-3-pentenyl, l-methyl-4-pentenyl, 2-methyl-4- pentenyl, 3-methyl-4-pentenyl, 4-methyl-4-pentenyl, l,l-dimethyl-2-butenyl, 1,1-dimethyl- 3-butenyl, 1,2-dimethyl- 1-butenyl, 1 ,2-dimethyI-2-butenyl, l,2-dimethyl-3-butenyl, 1,3- dimethyl- 1-butenyl, l,3-dimethyl-2-butenyl, 1, 3 -dimethy 1-3 -butenyl, 2,2-dimethyl-3- butenyl, 2,3-dimethyl- 1-butenyl, 2,3-dimethyl-2-butenyl, 2,3-dimethyl-3-butenyl, 3,3- dimethyl- 1-butenyl, 3,3-dimethyl-2-butenyl, 1 -ethyl- 1-butenyl, l-ethyl-2-butenyl, 1-ethyl- 3-butenyl, 2-ethyl- 1-butenyl, 2-ethyl-2-butenyl, 2-ethy 1-3 -butenyl, l,l,2-trimethyl-2- propenyl, 1 -ethyl- 1 -methyl- 2-propenyl, 1 -ethyl-2-methyl- 1 -propenyl and 1 -ethyl-2-methyl-2-propenyl groups.The term “alkynyl,” as used herein, refers to both straight and branched carbon chains which have at least one carbon-carbon triple bond. In one embodiment of alkynyl,the number of triple bonds is 1-3; in another embodiment of alkynyl, the number of triple bonds is one or two. In some embodiments, alkynyl groups include from C2-C20 alkynyl groups. In other embodiments, alkynyl groups may include C2-C12, C2-C10, C2-C8, C2-C6 or C2-C4 alkynyl groups. Other ranges of carbon-carbon triple bonds and carbon numbers are also contemplated depending on the location of the alkenyl moiety on the molecule. For example, the term ”C2-Cio-alkynyl” as used herein refers to a straight-chain or branched unsaturated hydrocarbon group having 2 to 10 carbon atoms and containing at least one triple bond, such as ethynyl, prop-l-yn-l-yl, prop-2-yn-l-yl, n-but-l-yn-l-yl, n-but-l-yn-3- yl, n-but-l-yn-4-yl, n-but-2-yn-l-yl, n-pent-l-yn-l-yl, n-pent-l-yn-3-yl, n-pent-l-yn-4-yl, n-pent-l-yn-5-yl, n-pent-2-yn-l-yl, n-pent-2-yn-4-yl, n-pent-2-yn-5-yl, 3-methylbut-l-yn-3- yl, 3-methylbut-l-yn-4-yl, n-hex-l-yn-l-yl, n-hex-l-yn-3-yl, n-hex-l-yn-4-yl, n-hex-l-yn- 5-yl, n-hex-l-yn-6-yl, n-hex-2-yn-l-yl, n-hex-2-yn-4-yl, n-hex-2-yn-5-yl, n-hex-2-yn-6-yl, n-hex-3-yn-l -yl, n-hex-3-yn-2-yl, 3-methylpent-l -yn-l -yl, 3-methylpent-l -yn-3-yl, 3- methylpent-l-yn-4-yl, 3-methylpent-l-yn-5-yl, 4-methylpent-l-yn-l-yl, 4-methylpent-2-yn- 4-yl, and 4-methylpent-2-yn-5-yl groups.The term “haloalkyl” or “alkylhalide,” as used herein refers to an alkyl group, as defined above, which is substituted by one or more halogen atoms. In some instances, the haloalkyl group can be an alkyl group substituted by one or more fluorine atoms. In certain instances, the haloalkyl group can be a perfluorinated alkyl group. For example, C1-C4- haloalkyl includes, but is not limited to, chloromethyl, bromomethyl, dichloromethyl, trichloromethyl, fluoromethyl, difluoromethyl, trifluoromethyl, chlorofluoromethyl, dichlorofluoromethyl, chlorodifluoromethyl, 1 -chloroethyl, 1 -bromoethyl, 1 -fluoroethyl, 2- fluoroethyl, 2,2-difluoroethyl, 2,2,2-trifluoroethyl, 2-chloro-2-fluoroethyl, 2-chloro-2,2- difluoroethyl, 2,2-dichloro-2-fluoroethyl, 2,2,2-trichloroethyl, and pentafluoroethyl.The term “alkoxy,” as used herein, refers to alkyl-O-, wherein alkyl refers to an alkyl group, as defined above. Similarly, the terms “alkenyloxy,” “alkynyloxy,” “haloalkoxy,” “haloalkenyloxy,” “haloalkynyloxy,” “cycloalkoxy,” “cycloalkenyloxy,” “halocycloalkoxy,” and “halocycloalkenyloxy” refer to the groups alkenyl-O-, alkynyl-O-, haloalkyl-O-, haloalkenyl-O-, haloalkynyl-O-, cycloalkyl-O-, cycloalkenyl-O-, halocycloalkyl-O-, and halocycloalkenyl-O-, respectively, wherein alkenyl, alkynyl, haloalkyl, haloalkenyl, haloalkynyl, cycloalkyl, cycloalkenyl, halocycloalkyl, and halocycloalkenyl are as defined above. Examples of Ci-Ce-alkoxy include, but are not limited to, methoxy, ethoxy, C2H5-CH2O-, (CFEhCHO-, n-butoxy, C2Hs-CH(CH3)O-,(CHibCH-CITC)-. (CH3)3CO-, n-pentoxy, 1 -methylbutoxy, 2-methylbutoxy, 3- methylbutoxy, 1 , 1 -dimethylpropoxy, 1,2-dimethylpropoxy, 2,2-dimethyl-propoxy, 1- ethylpropoxy, n-hexoxy, 1 -methylpentoxy, 2-methylpentoxy, 3-methylpentoxy, 4- methylpentoxy, 1,1 -dimethylbutoxy, 1 ,2-dimethylbutoxy, 1,3-dimethylbutoxy, 2,2- dimethylbutoxy, 2,3-dimethylbutoxy, 3,3-dimethylbutoxy, 1 -ethylbutoxy, 2-ethylbutoxy, 1,1,2-trimethylpropoxy, 1,2,2-trimethylpropoxy, 1 -ethyl- 1 -methylpropoxy, and l-ethyl-2- methylpropoxy.The terms “alkylamino” and “dialkylamino,” as used herein, refer to alkyl-NH- and (alkyl)oN- groups, where alkyl is as defined above. Similarly, the terms “haloalkylamino” and “halodialkylamino” refer to haloalkyl-NH- and (haloalky Ip-NH-, where haloalkyl is as defined above.The term “aryl,” as used herein, refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms. Aryl groups can include a single ring or multiple condensed rings. In some embodiments, aryl groups include Co-Cio aryl groups. Aryl groups include, but are not limited to, phenyl, biphenyl, naphthyl, tetrahydronaphtyl, phenylcyclopropyl and indanyl. Aryl groups may be unsubstituted or substituted by one or more moieties selected from halogen, cyano, nitro, hydroxy, mercapto, amino, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, haloalkyl, haloalkenyl, haloalkynyl, halocycloalkyl, halocycloalkenyl, alkoxy, alkenyloxy, alkynyloxy, haloalkoxy, haloalkenyloxy, haloalkynyloxy, cycloalkoxy, cycloalkenyloxy, halocycloalkoxy, halocycloalkenyloxy, alkylthio, haloalkylthio, cycloalkylthio, halocycloalkylthio, alkylsulfinyl, alkenylsulfinyl, alkynyl-sulfinyl, haloalkylsulfinyl, haloalkenylsulfinyl, haloalkynyl sulfinyl, alkylsulfonyl, alkenylsulfonyl, alkynylsulfonyl, haloalkyl-sulfonyl, haloalkenylsulfonyl, haloalky nylsulfonyl, alkylamino, alkenylamino, alkynylamino, di(alkyl)amino, di(alkenyl)-amino, di(alkynyl)amino, or trialkylsilyl.The term “alkylaryl,” as used herein, refers to an aryl group that is bonded to a parent compound through a diradical alkylene bridge, (-CH2- ), , where n is 1-12 and where “aryl” is as defined above.The term “alkylcycloalkyl,” as used herein, refers to a cycloalkyl group that is bonded to a parent compound through a diradical alkylene bridge, (-CH3-)n, where n is 1-12 and where “cycloalkyl” is as defined above. The term “cycloalkylalkyl,” as used herein, refers to a cycloalkyl group, as defined above, which is substituted by an alkyl group, as defined above.The term “heteroaryl,” as used herein, refers to a monovalent aromatic group of from 1 to 15 carbon atoms (e.g., from 1 to 10 carbon atoms, from 2 to 8 carbon atoms, from 3 to 6 carbon atoms, or from 4 to 6 carbon atoms) having one or more heteroatoms within the ring. The heteroaryl group can include from 1 to 4 heteroatoms, from 1 to 3 heteroatoms, or from 1 to 2 heteroatoms. In some cases, the heteroatom(s) incorporated into the ring are oxygen, nitrogen, sulfur, or combinations thereof. When present, the nitrogen and sulfur heteroatoms may optionally be oxidized. Heteroaryl groups can have a single ring (e.g., pyridyl or furyl) or multiple condensed rings provided that the point of attachment is through a heteroaryl ring atom. Preferred heteroaryls include pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, pyrrolyl, indolyl, quinolinyl, isoquinolinyl, quinazolinyl, quinoxalinyl, furanyl, thiophenyl, furyl, pyrrolyl, imidazolyl, oxazolyl, isoxazolyl, isothiazolyl, pyrazolyl, benzofuranyl, and benzothiophenyl. Heteroaryl rings may be unsubstituted or substituted by one or more moieties as described for aryl above.The term “alkylheteroaryl,” as used herein, refers to a heteroaryl group that is bonded to a parent compound through a diradical alkylene bridge, (-CH2-)n, where n is 1-12 and where “heteroaryl” is as defined above.The terms “cycloheteroalkyl,” “heterocyclyl,” “heterocyclic,” and “heterocyclo” are used herein interchangeably, and refer to fully saturated or unsaturated, cyclic groups, for example, 3- to 7-membered monocyclic or 4- to 7-membered monocyclic; 7- to 11- membered bicyclic, or 10- to 15-membered tricyclic ring systems, having one or more heteroatoms within the ring. The heterocyclyl group can include from 1 to 4 heteroatoms, from 1 to 3 heteroatoms, or from 1 to 2 heteroatoms. In some cases, the heteroatom(s) incorporated into the ring are oxygen, nitrogen, sulfur, or combinations thereof. When present, the nitrogen and sulfur heteroatoms may optionally be oxidized, and the nitrogen heteroatoms may optionally be quaternized. The heterocyclyl group may be attached at any heteroatom or carbon atom of the ring or ring system and may be unsubstituted or substituted by one or more moieties as described for aryl groups above.Exemplary monocyclic heterocyclic groups include, but are not limited to, pyrrolidinyl, pyrrolyl, pyrazolyl, oxetanyl, pyrazolinyl, imidazolyl, imidazolinyl, imidazolidinyl, oxazolyl, oxazolidinyl, isoxazolinyl, isoxazolyl, thiazolyl, thiadiazolyl, thiazolidinyl, isothiazolyl, isothiazolidinyl, furyl, tetrahydrofuryl, thienyl, oxadiazolyl, piperidinyl, piperazinyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolodinyl, 2- oxoazepinyl, azepinyl, 4-piperidonyl, pyridinyl, pyrazinyl, pyrimidinyl, pyridazinyl,tetrahydropyranyl, morpholinyl, thiamorpholinyl, thiamorpholinyl sulfoxide, thiamorpholinyl sulfone, 1,3-dioxolane and tetrahydro- 1,1 -dioxothienyl, triazolyl, triazinyl, and the like.The term “alkylheterocyclyl” and “alkylcycloheteroalkyl” are used herein interchangeably, and refer to a heterocyclyl group that is bonded to a parent compound through a diradical alkylene bridge, (-CH2-)n, where n is 1-12 and where “heterocyclyl” is as defined above. The term “heterocyclylalkyl,” as used herein, refers to a heterocyclyl group, as defined above, which is substituted by an alkyl group, as defined above.The term “halogen,” as used herein, refers to the atoms fluorine, chlorine, bromine and iodine. The prefix halo- (e.g., as illustrated by the term haloalkyl) refers to all degrees of halogen substitution, from a single substitution to a perhalo substitution (e.g., as illustrated with methyl as chloromethyl (-CH2CI), dichloromethyl (-CHQ2), trichloromethyl (-CCh)).As used herein, the term “substituted” is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, and aromatic and nonaromatic substituents of organic compounds. Illustrative substituents include, for example, those described below. The permissible substituents can be one or more and the same or different for appropriate organic compounds. For purposes of this disclosure, the heteroatoms, such as nitrogen, can have hydrogen substituents and / or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. This disclosure is not intended to be limited in any manner by the permissible substituents of organic compounds. Also, the terms “substitution” or “substituted with” include the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., a compound that does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc.The term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference.Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate , digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2- naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(C 1 4 alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.

[0015] The term “solvate” refers to forms of the compound that are associated with a solvent, usually by a solvolysis reaction. This physical association may include hydrogen bonding. Conventional solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and the like. The compounds of Formula (I) or (II) may be prepared, e.g., in crystalline form, and may be solvated. Suitable solvates include pharmaceutically acceptable solvates and further include both stoichiometric solvates and non- stoichiometric solvates. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid. “Solvate” encompasses both solution-phase and isolable solvates. Representative solvates include hydrates, ethanolates, and methanolates.The term “hydrate” refers to a compound that is associated with water. Typically, the number of the water molecules contained in a hydrate of a compound is in a definiteratio to the number of the compound molecules in the hydrate. Therefore, a hydrate of a compound may be represented, for example, by the general formula R x H2O, wherein R is the compound and wherein x is a number greater than 0. A given compound may form more than one type of hydrates, including, e.g., monohydrates (x is 1), lower hydrates (x is a number greater than 0 and smaller than 1, e.g., hemihydrates (R 0.5 H2O)), and polyhydrates (x is a number greater than 1, e.g., dihydrates (R-2 H2O) and hexahydrates (R- 6 H2O)).The term “tautomers” refer to compounds that are interchangeable forms of a particular compound structure, and that vary in the displacement of hydrogen atoms and electrons. Thus, two structures may be in equilibrium through the movement of n electrons and an atom (usually H). For example, enols and ketones are tautomers because they are rapidly interconverted by treatment with either acid or base. Another example of tautomerism is the aci- and nitro- forms of phenylnitromethane, that are likewise formed by treatment with acid or base. Tautomeric forms may be relevant to the attainment of the optimal chemical reactivity and biological activity of a compound of interest.It is also to be understood that compounds that have the same molecular formula but differ in the nature or sequence of bonding of their atoms or the arrangement of their atoms in space are termed “isomers.” Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.”Stereoisomers that are not mirror images of one another are termed “diastereomers” and those that are non- superimposable mirror images of each other are termed “enantiomers.” When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible. An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S- sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (z.e., as (+) or (-)- isomers respectively). A chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a “racemic mixture.”The term “polymorphs” refers to a crystalline form of a compound (or a salt, hydrate, or solvate thereof) in a particular crystal packing arrangement. All polymorphs have the same elemental composition. Different crystalline forms usually have different X- ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape,optical and electrical properties, stability, and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Various polymorphs of a compound can be prepared by crystallization under different conditions.The term “prodrugs” refer to compounds, including derivatives of the compounds of Formulae (I) and (II), which have cleavable groups and become by solvolysis or under physiological conditions the compounds of Formulae (I) and (II) which are pharmaceutically active in vivo. Such examples include, but are not limited to, ester derivatives, amide derivatives, and the like. Other derivatives of the compounds of this invention have activity in both their acid and acid derivative forms, but in the acid sensitive form often offers advantages of solubility, tissue compatibility, or delayed release in the mammalian organism (see Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well known to practitioners of the art, such as, for example, esters prepared by reaction of the parent acid with a suitable alcohol, or amides prepared by reaction of the parent acid compound with a substituted or unsubstituted amine, or acid anhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters, amides, and anhydrides derived from acidic groups pendant on the compounds of Formulae (I) and (II) are particular prodrugs.A “subject” to which administration is contemplated includes, but is not limited to, humans (e.g., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) and / or other non-human animals, for example, mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals, such as cattle, pigs, horses, sheep, goats, cats, and / or dogs) and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and / or turkeys). In certain embodiments, the animal is a mammal. The animal may be a male or female at any stage of development. A non-human animal may be a transgenic animal.The terms “administer,” “administering,” or “administration” refer to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing an inventive compound or a pharmaceutical composition thereof.The terms “treatment,” “treat,” and “treating” refer to reversing, alleviating, delaying the onset of, or inhibiting the progress of a “pathological condition” (e.g., metabolic disorders (e.g., obesity, diabetes), hypoxia related diseases (e.g., a proliferativedisease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder), or a disease resulting from rhodoquinone depletion (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, or neurodegenerative disorder), or one or more signs or symptoms thereof) described herein. In some embodiments, treatment may be administered after one or more signs or symptoms have developed or have been observed. In other embodiments, treatment may be administered in the absence of signs or symptoms of the disease or condition. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and / or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to delay or prevent recurrence.The term “prevent,” “preventing,” or “prevention” refers to a prophylactic treatment of a subject who does not have and did not have a disease but is at risk of developing the disease or is at risk of regression of the disease. In certain embodiments, the subject is at a higher risk of developing the disease or at a higher risk of regression of the disease than an average healthy member of a population.The terms “condition,” “disease,” and “disorder” are used interchangeably.An “effective amount” of a compound of Formula (I) or Formula (II) refers to an amount sufficient to elicit the desired biological response, e.g., activating the electron transport chain in a subject, tissue, or cell, or treating the condition, for example, treating a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound of Formula (I) or Formula (II) may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject. An effective amount encompasses therapeutic and prophylactic treatment. For example, in treating cancer, an effective amount of an inventive compound may reduce the tumor burden or stop the growth or spread of a tumor.A “therapeutically effective amount” of a compound of Formula (1) or Formula (11) is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or incombination with other therapies, which provides a therapeutic benefit in the treatment of the condition. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces, or avoids symptoms or causes of the condition, or enhances the therapeutic efficacy of another therapeutic agent.A “prophylactically effective amount” of a compound described herein is an amount sufficient to prevent a condition, or one or more signs or symptoms associated with the condition, or prevent its recurrence. A prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the condition. The term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.The term “biological sample” refers to any sample including organs, tissues, tissue samples (such as tissue sections and needle biopsies of a tissue); cell samples (e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection); samples of whole organisms (such as samples of yeasts or bacteria); or cell fractions, fragments, organelles (such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise). Other examples of biological samples include blood, serum, urine, semen, fecal matter, cerebrospinal fluid, interstitial fluid, mucus, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from a first biological sample. Biological samples also include those biological samples that are transgenic, such as a transgenic oocyte, sperm cell, blastocyst, embryo, fetus, donor cell, or cell nucleus, or cells or cell lines derived from biological samples.The term “tissue” refers to any biological tissue of a subject (including a group of cells, a body part, or an organ) or a part thereof, including blood and / or lymph vessels, which is the object to which a compound, and / or composition of the invention is delivered. A tissue may be an abnormal or unhealthy tissue, which may need to be treated. A tissue may also be a normal or healthy tissue that is under a higher than normal risk of becoming abnormal or unhealthy, which may need to be prevented. In certain embodiments, the tissue is the central nervous system. In certain embodiments, the tissue is the brain. In certain embodiments, the tissue is an organ. In certain embodiments, the organ is an ex vivo organ (e.g., an organ being transported and / or stored for organ transplant).The term “hypoxia” or “hypoxic condition” as used herein refers to a state or condition in which oxygen in a subject or in one or more tissues of a mammal is below the physiologic levels of oxygen in that tissue, e.g., is at a less than optimal level. Hypoxia can also be defined as a state in which reactions that require O2 are hindered due to allosteric inhibition by other metabolites or direct inactivation, such as by high levels of reactive oxygen species. In some embodiments, hypoxia may result from stress such as aerobic exercise, physical weight pressure, anesthesia, surgery, anemia, acute respiratory distress syndrome, chronic illness, chronic fatigue syndrome, trauma, bums, skin ulcers, cachexia due to cancer and other catabolic states and the like. In certain embodiments, hypoxia may result from a complete or partial blockage of a blood vessel, abnormally low blood pressure, vasoconstriction, reduced air flow in and out of the lungs, or damaged lung tissue. In certain embodiments, the hypoxia can be caused by a stroke, myocardial infarction, heart failure, blood disorder such as sickle cell anemia, or trauma.In some embodiments, hypoxia is or comprises “ischemia” or “ischemic conditions” in which tissues are oxygen-deprived due to reduction in blood flow, as due to constriction in, or blockage of, a blood vessel. Ischemia or ischemic conditions include those caused by coronary artery disease, cardiomyopathy, including alcoholic cardiomyopathy, angioplasty, stenting, heart surgery such as bypass surgery or heart repair surgery (“openheart surgery”), organ transplantation, prolonged weight pressure on tissues (pressure ulcers or bedsores), ischemia-reperfusion injury which can cause damage to transplanted organs or tissue, and the like.In some embodiments, treatments described herein may, for example, increase energy level, strength and / or well-being of a subject suffering from hypoxia even if they do not treat one or more aspects of an underlying condition (e.g., viral or bacterial infection, exposure to bacterial or other toxins, low red-cell counts, aging, cancer, continued exercise, high altitude exercise).In some embodiments, the terms “hypoxia” or “hypoxic condition” refer to a condition of low oxygen content in the blood. In some embodiments, hypoxia or hypoxic conditions may be defined by arterial PO2 values less than approximately 80 mm Hg and venous PO2 values less than approximately 30 mm Hg. In some embodiments, hypoxia or hypoxic conditions may be defined by arterial PO2 values less than approximately 60 mm Hg. In certain embodiments, hypoxia or hypoxic conditions may be defined by arterial PO2 values less than approximately 50 mm Hg. In a particular embodiment, hypoxia or hypoxicconditions may be defined by arterial PO2 values between approximately 50-20 mm Hg. In certain cases, hypoxia or hypoxic conditions may be defined by intra-tissue PO2 levels less than about 10 mm Hg. In some embodiments, hypoxia or hypoxic conditions may be defined by intra-tissue PO2 levels less than about 5 mm Hg. In some embodiments, hypoxia or hypoxic conditions may be defined by intra-tumor PO2 levels less than about 10 mm Hg. In some embodiments, hypoxia or hypoxic conditions may be defined by intra-tumor PO2 levels less than about 5 mm Hg.Hypoxia or hypoxic conditions may be chronic or acute. “Chronic hypoxia,” as used herein, may refer to sustained hypoxic conditions that result in a measurable increase in 2HG and / or lactate production. That is, chronic hypoxia may be defined as hypoxic conditions of sufficient duration to allow 2HG and / or lactate to accumulate above baseline levels. In some embodiments, chronic hypoxia is a hypoxic condition of more than 15 minutes, 30 minutes, more than 1 hour, more than 2 hours, more than 3 hours, more than 4 hours, more than 5 hours, more than 10 hours, more than 12 hours, more than 24 hours, more than a day, or a week or more in duration. In some embodiments, chronic hypoxia is caused by consumption and depletion of oxygen by tissues or tumor cells between blood capillaries and the hypoxic regions. In contrast to the sustained conditions of chronic hypoxia, acute hypoxia is transient. In some embodiments, acute hypoxia occurs when there a temporary shutdown of vessels or microvasculature in tissues or tumors. In some embodiments, acute hypoxia occurs as a result of fluctuations in red blood cell levels.A “hypoxia related disease” is a disease, disorder, or condition associated with (e.g., whose incidence or severity correlates with and / or that is characterized by one or more aspects of) hypoxia. In some particular embodiments, a hypoxia related disease, disorder or condition may be or comprise, for example, septic shock, ischemic stroke, myocardial infarction, anemia, pulmonary disease, airway obstruction, acute respiratory distress syndrome, pneumonia, pneumothorax, emphysema, congenital heart defects, atherosclerosis, thrombosis, pulmonary embolism, pulmonary edema, asthma, cystic fibrosis, cancer, certain surgical procedures. In some embodiments, a hypoxia related disease, disorder or condition is associated with stress such as aerobic exercise, physical weight pressure, anesthesia, surgery, anemia, acute respiratory distress syndrome, chronic illness, chronic fatigue syndrome, trauma, burns, skin ulcers, cachexia due to cancer and other catabolic states and the like. In some embodiments, a hypoxia-related disease, disorder or condition is or comprises “ischemia” or “ischemic conditions” in which tissuesare oxygen-deprived due to reduction in blood flow, as due to constriction in, or blockage of, a blood vessel. Ischemia or ischemic conditions include those caused by coronary artery disease, cardiomyopathy, including alcoholic cardiomyopathy, angioplasty, stenting, heart surgery such as bypass surgery or heart repair surgery (“open-heart surgery”), organ transplantation, prolonged weight pressure on tissues (pressure ulcers or bedsores), ischemia-reperfusion injury which can cause damage to transplanted organs or tissue, and the like.Without wishing to be bound by any particular theory, unwanted depletion of bacteria that produce this rhodoquinone and / or rhodoquinol may have severe implications for mitochondrial function in organs that rely on rhodoquinone as an electron carrier. Thus, the loss of this metabolite after antibiotic treatment may affect patient risk for diseases related to ischemia, and supplementation with a rhodoquinone mimetic as described herein may protect those subjects.The term "metabolic disorder" refers to any disorder that involves an alteration in the normal metabolism of carbohydrates, lipids, sterols, amino acids, reactive oxygen species, cofactors, proteins, nucleic acids, or a combination thereof. In some embodiments, the metabolite can be a small molecule having a molecular weight of 2500 Da or less. A metabolic disorder is associated with either a deficiency or excess in a metabolic pathway resulting in an imbalance in metabolism of nucleic acids, proteins, lipids, and / or carbohydrates. Factors affecting metabolism include, and are not limited to, the endocrine (hormonal) control system (e.g., the insulin pathway, the enteroendocrine hormones including GLP-1, PYY or the like), the neural control system (e.g., GLP-1 in the brain), or the like. Examples of metabolic disorders include, but are not limited to, diabetes (e.g., Type I diabetes, Type II diabetes, gestational diabetes), hyperglycemia, hyperinsulinemia, insulin resistance, and obesity.A “proliferative disease” refers to a disease that occurs due to abnormal growth or extension by the multiplication of cells (Walker, Cambridge Dictionary of Biology, Cambridge University Press: Cambridge, UK, 1990). A proliferative disease may be associated with: 1) the pathological proliferation of normally quiescent cells; 2) the pathological migration of cells from their normal location (e.g., metastasis of neoplastic cells); 3) the pathological expression of proteolytic enzymes, such as the matrix metalloproteinases (e.g., collagenases, gelatinases, and elastases); or 4) the pathological angiogenesis as in proliferative retinopathy and tumor metastasis. Exemplary proliferativediseases include cancers (e.g., “malignant neoplasms”), benign neoplasms, lymphoma, nonHodgkin’s lymphoma, leukemia, sarcoma, lung cancer, thyroid cancer, breast cancer, liver cancer, pancreatic cancer, gastric cancer, ovarian cancer, colon cancer, colorectal cancer, skin cancer, esophageal cancer, and carcinoma. Exemplary proliferative diseases include cancers (e.g., “malignant neoplasms,” sarcoma, lung cancer, thyroid cancer, breast cancer, liver cancer, pancreatic cancer, gastric cancer, ovarian cancer, colon cancer, colorectal cancer, skin cancer, esophageal cancer; carcinoma), benign neoplasms, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases.The terms “neoplasm” and “tumor” are used herein interchangeably and refer to an abnormal mass of tissue wherein the growth of the mass surpasses and is not coordinated with the growth of a normal tissue. A neoplasm or tumor may be “benign” or “malignant,” depending on the following characteristics: degree of cellular differentiation (including morphology and functionality), rate of growth, local invasion, and metastasis. A “benign neoplasm” is generally well differentiated, has characteristically slower growth than a malignant neoplasm, and remains localized to the site of origin. In addition, a benign neoplasm does not have the capacity to infiltrate, invade, or metastasize to distant sites. Exemplary benign neoplasms include, but are not limited to, lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheic keratoses, lentigos, and sebaceous hyperplasias. In some cases, certain “benign” tumors may later give rise to malignant neoplasms, which may result from additional genetic changes in a subpopulation of the tumor’s neoplastic cells, and these tumors are referred to as “pre-malignant neoplasms.” An exemplary pre- malignant neoplasm is a teratoma. In contrast, a “malignant neoplasm” is generally poorly differentiated (anaplasia) and has characteristically rapid growth accompanied by progressive infiltration, invasion, and destruction of the surrounding tissue. Furthermore, a malignant neoplasm generally has the capacity to metastasize to distant sites. The term “metastasis,” “metastatic,” or “metastasize” refers to the spread or migration of cancerous cells from a primary original tumor to another organ or tissue and is typically identifiable by the presence of a “secondary tumor” or “secondary cell mass” of the tissue type of the primary original tumor and not of that of the organ or tissue in which the secondary (metastatic) tumor is located. For example, a prostate cancer that has migrated to bone is said to be metastasized prostate cancer and includes cancerous prostate cancer cells growing in bone tissue.The term “cancer” refers to a malignant neoplasm Stedman ’s Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia, 1990). Exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendothelio sarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma; chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma); connective tissue cancer; epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi’s sarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett’s adenocarcinoma); Ewing’s sarcoma; eye cancer (e.g., intraocular melanoma, retinoblastoma); familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g., stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germ cell cancer; head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)); hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T- cell CLL)); lymphoma such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B-cell lymphoma), follicular lymphoma, chronic lymphocytic leukemia / small lymphocytic lymphoma (CLL / SLL), MYD88-mutated Waldenstrom’s macroglobulinemia, activated B-cell (ABC) diffuse large B-cell lymphoma, mantle cell lymphoma (MCL), marginal zone B-cell lymphomas (e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodal marginal zone B-cell lymphoma, splenic marginal zone B- cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma ( / '.<?., Waldenstrom’s macroglobulinemia), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B -lymphoblasticlymphoma and primary central nervous system (CNS) lymphoma; and T-cell NHL such as precursor T- lymphoblastic lymphoma / leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T- cell lymphoma (CTCL) (e.g., mycosis fungoides, Sezary syndrome), angioimmunoblastic T- cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathy type T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplastic large cell lymphoma); a mixture of one or more leukemia / lymphoma as described above; and multiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease); hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastic tumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms’ tumor, renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreatic neuroendocrinetumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer (e.g., Paget’s disease of the penis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplastic syndromes; intraepithelial neoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g., appendix cancer); soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestine cancer; sweat gland carcinoma; synovioma; testicular cancer (e.g., seminoma, testicular embryonal carcinoma); thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroidcarcinoma (PTC), medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvar cancer (e.g., Paget’s disease of the vulva).The term “inflammatory disease” refers to a disease caused by, resulting from, or resulting in inflammation. The term “inflammatory disease” may also refer to a dysregulated inflammatory reaction that causes an exaggerated response by macrophages, granulocytes, and / or T-lymphocytes leading to abnormal tissue damage and / or cell death. An inflammatory disease can be either an acute or chronic inflammatory condition and can result from infections or non-infectious causes. Inflammatory diseases include, without limitation, atherosclerosis, arteriosclerosis, autoimmune disorders, multiple sclerosis, systemic lupus erythematosus, polymyalgia rheumatic (PMR), gouty arthritis, degenerative arthritis, tendonitis, bursitis, psoriasis, cystic fibrosis, arthrosteitis, rheumatoid arthritis, inflammatory arthritis, Sjogren’s syndrome, giant cell arteritis, progressive systemic sclerosis (scleroderma), ankylosing spondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid, diabetes (e.g., Type I), myasthenia gravis, Hashimoto’s thyroiditis, Graves’ disease, Goodpasture’s disease, mixed connective tissue disease, sclerosing cholangitis, inflammatory bowel disease, Crohn’s disease, ulcerative colitis, pernicious anemia, inflammatory dermatoses, usual interstitial pneumonitis (UIP), asbestosis, silicosis, bronchiectasis, berylliosis, talcosis, pneumoconiosis, sarcoidosis, desquamative interstitial pneumonia, lymphoid interstitial pneumonia, giant cell interstitial pneumonia, cellular interstitial pneumonia, extrinsic allergic alveolitis, Wegener’s granulomatosis and related forms of angiitis (temporal arteritis and polyarteritis nodosa), inflammatory dermatoses, hepatitis, delayed-type hypersensitivity reactions (e.g., poison ivy dermatitis), pneumonia, respiratory tract inflammation, Adult Respiratory Distress Syndrome (ARDS), encephalitis, immediate hypersensitivity reactions, asthma, hayfever, allergies, acute anaphylaxis, rheumatic fever, glomerulonephritis, pyelonephritis, cellulitis, cystitis, chronic cholecystitis, ischemia (ischemic injury), reperfusion injury, allograft rejection, host-versus-graft rejection, appendicitis, arteritis, blepharitis, bronchiolitis, bronchitis, cervicitis, cholangitis, chorioamnionitis, conjunctivitis, dacryoadenitis, dermatomyositis, endocarditis, endometritis, enteritis, enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis, gingivitis, ileitis, iritis, laryngitis, myelitis, myocarditis, nephritis, omphalitis, oophoritis, orchitis, osteitis, otitis, pancreatitis, parotitis, pericarditis, pharyngitis, pleuritis, phlebitis, pneumonitis, proctitis, prostatitis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis, testitis, tonsillitis, urethritis, urocystitis, uveitis, vaginitis,vasculitis, vulvitis, vulvovaginitis, angitis, chronic bronchitis, osteomyelitis, optic neuritis, temporal arteritis, transverse myelitis, necrotizing fasciitis, and necrotizing enterocolitis. An ocular inflammatory disease includes, but is not limited to, post-surgical inflammation. In certain embodiments, the inflammatory disorder is fibrosis, and the fibrosis is idiopathic pulmonary fibrosis, liver cirrhosis, cystic fibrosis, systemic sclerosis, progressive kidney disease, or cardiovascular fibrosis.The term “therapeutic agent” refers to any substance having therapeutic properties that produce a desired, usually beneficial, effect. For example, therapeutic agents may treat, ameliorate, and / or prevent disease. Therapeutic agents, as disclosed herein, may be biologies or small molecule therapeutics.“Administration" to a subject includes any route of introducing or delivering to a subject an agent. Administration can be carried out by any suitable route, including oral, topical, intravenous, subcutaneous, transcutaneous, transdermal, intramuscular, intra-joint, intra- arteriole, intradermal, intraventricular, intracranial, intraperitoneal, intralesional, intranasal, rectal, vaginal, by inhalation, via an implanted reservoir, parenteral (e.g., subcutaneous, intravenous, intramuscular, intra- articular, intra-synovial, intrasternal, intrathecal, intraperitoneal, intrahepatic, intralesional, and intracranial injections or infusion techniques), and the like. "Concurrent administration", "administration in combination", "simultaneous administration" or "administered simultaneously" as used herein, means that the compounds are administered at the same point in time or essentially immediately following one another. In the latter case, the two compounds are administered at times sufficiently close that the results observed are indistinguishable from those achieved when the compounds are administered at the same point in time. "Systemic administration" refers to the introducing or delivering to a subject an agent via a route which introduces or delivers the agent to extensive areas of the subject's body (e.g. greater than 50% of the body), for example through entrance into the circulatory or lymph systems. By contrast, "local administration" refers to the introducing or delivery to a subject an agent via a route which introduces or delivers the agent to the area or area immediately adjacent to the point of administration and does not introduce the agent systemically in a therapeutically significant amount. For example, locally administered agents are easily detectable in the local vicinity of the point of administration but are undetectable or detectable at negligible amounts in distal parts of the subject's body. Administration includes self-administration and the administration by another.CompoundsProvided herein are compounds (rhodoquinone mimetics) defined by Formula I orFormula II belowor a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from, Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhe tercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; R1is chosen from Ci-Ce alkyl and Ci-Ce haloalkyl; R2and R2are independently chosen from hydrogen, C i -Ce alkyl, and C i -Ce haloalkyl, or R2and R2, together with the nitrogen atom to which they are attached, combine to form a 3 to 7 membered heterocycloalkyl ring; R3is chosen from hydrogen, Ci-Ce alkyl, and Ci-Ce haloalkyl; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, Ci-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkylthio, Cue alkylsulfinyl, Cn 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(C 1-6 alky IJcarbamyl, carboxy, C1-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, Ci .6 alkylaminosulfonylamino, di(Ci-6 alkyl)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.In some embodiments of Formula I and Formula II, R1can be methyl. In some embodiments of Formula I and Formula II, R1can be CF3.In some embodiments of Formula I and Formula II, R2and R2can be hydrogen.In some embodiments of Formula I and Formula II, R3can be methyl.In some embodiments of Formula I and Formula II, R3can be CF3.In some embodiments of Formula I and Formula II, R1can be methyl, and R2and R2can be hydrogen.In some embodiments of Formula I and Formula II, R1can be CF3, and R2and R2can be hydrogen.In some embodiments of Formula I and Formula II, R1can be methyl, and R3can be methyl.In some embodiments of Formula I and Formula II, R1can be CF3, and R3can be methyl.In some embodiments of Formula I and Formula II, R1can be methyl, and R3can be CF3.In some embodiments of Formula I and Formula II, R1can be CF3, and R3can be CF3.In some embodiments of Formula I and Formula II, R2and R2can be hydrogen, and R3can be methyl.In some embodiments of Formula I and Formula II, R2and R2can be hydrogen, and R3can be CF3.In some embodiments of Formula I and Formula II, R1can be methyl, R2and R2can be hydrogen, and R3can be methyl.In some embodiments of Formula I and Formula II, R1can be CF3, R2and R2can be hydrogen, and R3can be methyl.In some embodiments of Formula I and Formula II, R1can be methyl, R2and R2can be hydrogen, and R3can be CF3.In some embodiments of Formula I and Formula II, R1can be CF3, R2and R2can be hydrogen, and R3can be CF3.In some embodiments of Formula I and Formula II, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups.In certain embodiments of Formula I and Formula II, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-i8 alkyl, Ce-12 alkyl, or Cs-i6 alkyl) optionally substituted by 1, 2, or 3 independently selected RAgroups.In certain embodiments of Formula I and Formula II, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-n alkyl, or Cs-i6 alkyl).In certain embodiments of Formula I and Formula II, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-i8 alkyl, Ce-i2 alkyl, or Cs-i6 alkyl) substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by a hydroxy group).In some embodiments of Formula I and Formula II, Z can be Ce-24 alkylaryl optionally substituted by 1, 2, or 3 independently selected RAgroups.In certain embodiments of Formula I and Formula II, Z is Ce-24 heteroalkyl (e.g., Ce- 18 heteroalkyl, Cs-is heteroalkyl, Ce-12 heteroalkyl, or Cs-ie heteroalkyl). In some of these embodiments, the heteroalky] group can comprise an oligo- or polyalkyleneoxy group.In other embodiments of Formula I and Formula II, Z isIn some of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula I and Formula II, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula I and Formula II, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula I and Formula II where Z is, the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can be defined by Formula IA or Formula IIA belowor a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from / x L / A, Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, CM haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkylthio, C1-6 alkylsulfinyl, Ci- 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(Ci-6alkyl)carbamyl, carboxy, C1-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, CM alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(C alkyl)aminosulfonyl, aminosulfonylamino, Ci -6 alkylaminosulfonylamino, di(Ci-6 alkyl)aminosulfonylamino, aminocarbonylamino, C alkylaminocarbonylamino, and di(Ci e alkyl)aminocarbonylamino.In some embodiments of Formula IA and Formula IIA, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IA and Formula IIA, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-i2 alkyl, or Cs-ie alkyl). In certain embodiments of Formula IA and Formula IIA, Z is Ce- 24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-is heteroalkyl, Ce-12 heteroalkyl, or Cs-ie heteroalkyl).In other embodiments of Formula IA and Formula IIA, Z is. In some of these embodiments, L is absent. In other of these embodiments, L can be a linking groupcomprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula IA and Formula IIA, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IA and Formula IIA, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula IA and Formula IIA where Z is;the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can be defined by Formula IB or Formula IIB belowFormula IB Formula IIB or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is chosen from / x L / A, C6-24 alkyl, C6-24 alkynyl, C6-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkyl thio, C1-6 alkylsulfinyl, Ci 6 alkylsulfonyl, carbamyl, C1-6 alkylcarbamyl, di(C 1-6 alky IJcarbamyl, carboxy, C1-6alkylcarbonyl, Ci-6 alkoxycarbonyl, Ci-6 alkylcarbonylamino, Ci -6 alkylsulfonylamino, aminosulfonyl, Ci -6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, Ci -6 alkylaminosulfonylamino, di(Ci-6 alkyl)aminosulfonylamino, aminocarbonylamino, Ci-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.In some embodiments of Formula IB and Formula IIB, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IB and Formula IIB, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-i2 alkyl, or Cs-ie alkyl). In certain embodiments of Formula IB and Formula IIB, Z is Ce- 24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-is heteroalkyl, Ce-i2 heteroalkyl, or Cs-ie heteroalkyl). In certain embodiments of Formula IB and Formula IIB, Z can be Ce-24 alkyl, optionally substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by a hydroxy group). In certain embodiments of Formula IB and Formula IIB, Z can be Ce-24 alkylaryl, optionally substituted by 1, 2, or 3 independently selected RAgroups.In other embodiments of Formula IB and Formula IIB, Z is. In some of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula IB and Formula IIB, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IB and Formula IIB, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula IB and Formula IIB where Z is, the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can be defined by Formula IC or Formula IIC belowFormula IC Formula IIC or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein Z is / Achosen from L , Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups; L is absent, or represents a bivalent linking group; A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6 haloalkoxy, cyano-Ci-3 alkyl, HO-Ci 3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C 1-6 alkylthio, C1-6 alkylsulfinyl, Ci- 6 alkylsulfonyl, carbamyl, C 1-6 alkylcarbamyl, di(Ci-6 alkyl)carbamyl, carboxy, Ci-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, Ci -6 alkylaminosulfonylamino, di(C 1-6 alky l)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.In some embodiments of Formula IC and Formula IIC, Z can be Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IC and Formula IIC, Z is Ce-24 alkyl (e.g., Ce-is alkyl, Cs-is alkyl, Ce-12 alkyl, or Cs-i6 alkyl). In certain embodiments of Formula IC and Formula IIC, Z is Ce- 24 heteroalkyl (e.g., Ce-is heteroalkyl, Cs-is heteroalkyl, Ce-i2 heteroalky], or Cs-ie heteroalkyl). In certain embodiments of Formula IC and Formula IIC, Z can be Ce-24 alkyl, optionally substituted by 1, 2, or 3 independently selected RAgroups (e.g., substituted by ahydroxy group). In certain embodiments of Formula IC and Formula IIC, Z can be Ce-24 alkylaryl, optionally substituted by 1, 2, or 3 independently selected RAgroups.In other embodiments of Formula IC and Formula IIC, Z is. In some of these embodiments, L is absent. In other of these embodiments, L can be a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms. In certain embodiments of Formula IC and Formula IIC, L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups. In certain embodiments of Formula IC and Formula IIC, L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.In some embodiments of Formula IC and Formula IIC where Z is, the mitochondrial targeting moiety can comprise a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof. In certain embodiments, the mitochondrial targeting moiety can comprise a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation. In certain embodiments, the mitochondrial targeting moiety can comprise a Szeto-Shiller peptide.In some embodiments, the compound can comprise one of the following:wherein n is an integer from 3 to 18, Ph represents phenyl, and TPP represents a triphenylphosphonium cation.In the formulae above, the linking group, when present, can be any suitable group or moiety which is at minimum bivalent, and connects the two radical moieties to which the linking group is attached. The linking group can be composed of any assembly of atoms, including oligomeric and polymeric chains. In some cases, the total number of atoms in the linking group can be from 3 to 200 atoms (e.g., from 3 to 150 atoms, from 3 to 100 atoms, from 3 and 50 atoms, from 3 to 25 atoms, from 3 to 15 atoms, or from 3 to 10 atoms).In some embodiments, the linking group can be, for example, an alkyl, alkoxy, alkylaryl, alkylheteroaryl, alkylcycloalkyl, alkylheterocycloalkyl, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, dialkylamino, alkylcarbonyl, alkoxycarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, or polyamino group. In some embodiments, the linking group can comprises one of the groups above joined to one or both of the moieties to which it is attached by a functional group. Examples of suitable functional groups include, for example, secondary amides (-CONH-), tertiary amides (-CONR-), secondary carbamates (-OCONH-; -NHCOO-), tertiary carbamates (-OCONR-; -NRCOO-), ureas (-NHCONH-; -NRCONH-; -NHCONR-, or -NRCONR-), carbinols ( -CHOH-, - CROH-), ethers (-O-), and esters (-COO-, -CH2O2C-, CHRO2C-), wherein R is an alkyl group, an aryl group, or a heterocyclic group. For example, in some embodiments, the linking group can comprise an alkyl group (e.g., a C1-C12 alkyl group, a Ci-Cs alkyl group, or a Ci-Ce alkyl group) bound to one or both of the moieties to which it is attached via an ester (-COO-, -CH2O2C-, CHRO2C-), a secondary amide (-CONH-), or a tertiary amide (- CONR-), wherein R is an alkyl group, an aryl group, or a heterocyclic group.In certain embodiments, the linking group can be chosen from one of the following:where m is an integer from 1 to 12 and R1is, independently for each occurrence, hydrogen, an alkyl group, an aryl group, or a heterocyclic group.In certain embodiments, the linking group can be chosen from optionally substituted -Cl-10 alkylene-, -O-Cl-10 alkylene-, -Cl-10 alkenylene-, -O-Cl-10 alkenylene-, -Cl-10 alkynylene-, -O-Cl-10 alkynylene-, -arylene-, -heteroarylene-, -cycloalkylene-, - heterocycloalkylene-, -O-, -S-, -S-S-, -S(O)W-, -C(O)-, -C(O)O-, -OC(O)-, -C(O)S-, - SC(O)-, -OC(O)O-, -N(Rb)-, -C(O)N(Rb)-, -N(Rb)C(O)-, -OC(O)N(Rb)-, -N(Rb)C(O)O-, - SC(O)N(Rb)-, -N(Rb)C(O)S-, -N(Rb)C(O)N(Rb)-, -N(Rb)C(NRb)N(Rb)-, -N(Rb)S(O)w- , - S(O)wN(Rb)-, -S(O)WO-, -OS(O)W-, -OS(O)WO-, -O(O)P(ORb)O-, (O)P(O-)3, - O(S)P(ORb)O-, and (S)P(O-)3, wherein w is 1 or 2, and Rbis independently hydrogen, optionally substituted alkyl, or optionally substituted aryl;In certain embodiments, the linking group can be chosen from optionally substituted -Cl-10 alkynylene-, -O-Cl-10 alkynylene-, -arylene-, -heteroarylene-, -cycloalkylene-, and -heterocycloalkylene-.In some embodiments, the linking group can bem, where m is an integer from1 to 12 (e.g., an integer from 1 to 6, or an integer from 1 to 3). In certain embodiments, the linking group canIf desired, the linker can serve to modify the solubility of the compounds described herein. In some embodiments, the linker is hydrophilic. In some embodiments, the linker can be an alkyl group, an alkylaryl group, an oligo- or polyalkylene oxide chain (e.g., an oligo- or polyethylene glycol chain), or an oligo- or poly(amino acid) chain.In the formulae above, the mitochondrial targeting moiety can comprise any suitable moiety that can direct the attached rhodoquinone mimetic to the mitochondria of a cell. As used herein, “targeting” means that the rhodoquinone mimetic accumulates in mitochondria relative to other organelles or cytoplasm at a greater concentration than substantially similar non-targeted rhodoquinone mimetic. A substantially similar non-targeted rhodoquinone mimetic includes an otherwise identical compound of Formula I or Formula II but lacking the targeting moiety.Examples of mitochondrial targeting moieties are known in the art. Due to the substantial negative electrochemical potential maintained across the inner mitochondrial membrane, delocalized lipophilic cations are effective at crossing the hydrophobic membranes and accumulating in the mitochondria. For example, triphenyl phosophonium (TPP) containing compounds can accumulate greater than 10 fold within the mitochondrial matrix. Any suitable TPP-containing compound such as N-(2- hydroxylpropyl) methacrylamide (HPMA)-TPP may be used as a mitochondrial matrix targeting moiety. Other suitable examples of delocalized lipophilic cations include rhodamine cations, such as Rhodamine 123.Of course, non-cationic compounds may serve to target and accumulate in the mitochondrial matrix. By way of example, Szeto-Shiller peptides may serve to target and accumulate a nanoparticle in the mitochondrial matrix. Any suitable Szetto-Shiller peptide may be employed as a mitochondria] matrix targeting moiety. Non-limiting examples of suitable Szeto-Shiller peptides include SS-02 and SS-31.Pharmaceutical Compositions and KitsAlso provided are pharmaceutical compositions comprising a compound (rhodoquinone mimetic) described herein and optionally a pharmaceutically acceptable excipient. In certain embodiments, the composition can further comprise an additional pharmaceutical agent.The compound (rhodoquinone mimetic) can be provided in an effective amount in the pharmaceutical composition. In certain embodiments, the effective amount is a therapeutically effective amount. In certain embodiments, the effective amount is a prophylactically effective amount.Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include bringing the compound described herein (z.e., the “active ingredient”) into association with a carrier or excipient, and / or one or more other accessory ingredients, and then, if necessary and / or desirable, shaping, and / or packaging the product into a desired single- or multi-dose unit.Pharmaceutical compositions can be prepared, packaged, and / or sold in bulk, as a single unit dose, and / or as a plurality of single unit doses. A “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the activeingredient which would be administered to a subject and / or a convenient fraction of such a dosage, such as one-half or one-third of such a dosage.Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and / or any additional ingredients in a pharmaceutical composition described herein will vary, depending upon the identity, size, and / or condition of the subject treated and further depending upon the route by which the composition is to be administered. The composition may comprise between 0.1% and 100% (w / w) active ingredient.Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and / or granulating agents, surface active agents and / or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and / or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.Exemplary granulating and / or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose, and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, crosslinked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, and mixtures thereof.Exemplary surface active agents and / or emulsifiers include natural emulsifiers (e.g., acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminum silicate)), long chain amino acid derivatives, high molecular weight alcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g.,carboxy polymethylene, poly aery lie acid, acrylic acid polymer, and carboxy vinyl polymer), carrageenan, cellulosic derivatives (e.g., carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g., polyoxyethylene sorbitan monolaurate (Tween® 20), polyoxyethylene sorbitan (Tween® 60), polyoxyethylene sorbitan monooleate (Tween® 80), sorbitan monopalmitate (Span® 40), sorbitan monostearate (Span® 60), sorbitan tristearate (Span® 65), glyceryl monooleate, sorbitan monooleate (Span® 80), polyoxyethylene esters (e.g., polyoxyethylene monostearate (Myrj® 45), polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol®), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g., Cremophor®), polyoxyethylene ethers, (e.g., polyoxyethylene lauryl ether (Brij® 30)), poly (vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic® F-68, poloxamer P-188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, and / or mixtures thereof.

[0115] Exemplary binding agents include starch (e.g., cornstarch and starch paste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g., acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly (vinyl-pyrrolidone), magnesium aluminum silicate (Veegum®), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, and / or mixtures thereof.Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, antiprotozoan preservatives, alcohol preservatives, acidic preservatives, and other preservatives. In certain embodiments, the preservative is an antioxidant. In other embodiments, the preservative is a chelating agent.Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, betacarotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant® Plus, Phenonip®, methylparaben, Germall® 115, Germaben® II, NeoIone®, Kathon®, and Euxyl®.Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D- gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate,sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer’ s solution, ethyl alcohol, and mixtures thereof.Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, and mixtures thereof.Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils. Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixtures thereof.Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredients, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3 -butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, com, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the conjugates described herein are mixed with solubilizing agents such as Cremophor®, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and mixtures thereof.Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension, or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3 -butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer’s solution, U.S.P., and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or di-glycerides. In addition, fatty acids such as oleic acid are used in the preparation of injec tables.The injectable formulations can be sterilized, for example, by filtration through a bacterial -retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This can be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution, which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form may be accomplished by dissolving or suspending the drug in an oil vehicle.Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates described herein with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol, or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and / or (a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, (b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, (c) humectants such as glycerol, (d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch,alginic acid, certain silicates, and sodium carbonate, (e) solution retarding agents such as paraffin, (f) absorption accelerators such as quaternary ammonium compounds, (g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolin and bentonite clay, and (i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets, and pills, the dosage form may include a buffering agent.Solid compositions of a similar type can be employed as fillers in soft and hard- filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the art of pharmacology. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of encapsulating compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.The compound (rhodoquinone mimetic) described herein can be in a micro- encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings, and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose, or starch. Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of encapsulating agents which can be used include polymeric substances and waxes.Dosage forms for topical and / or transdermal administration of a compound described herein may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants, and / or patches. Generally, the active ingredient is admixed under sterileconditions with a pharmaceutically acceptable carrier or excipient and / or any needed preservatives and / or buffers as can be required. Additionally, the present disclosure contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body. Such dosage forms can be prepared, for example, by dissolving and / or dispensing the active ingredient in the proper medium. Alternatively or additionally, the rate can be controlled by either providing a rate controlling membrane and / or by dispersing the active ingredient in a polymer matrix and / or gel.Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin. Alternatively or additionally, conventional syringes can be used in the classical mantoux method of intradermal administration. Jet injection devices which deliver liquid formulations to the dermis via a liquid jet injector and / or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable. Ballistic powder / particle delivery devices which use compressed gas to accelerate the compound in powder form through the outer layers of the skin to the dermis are suitable.Formulations suitable for topical administration include, but are not limited to, liquid and / or semi-liquid preparations such as liniments, lotions, oil-in-water and / or water- in- oil emulsions such as creams, ointments, and / or pastes, and / or solutions and / or suspensions. Topically administrable formulations may, for example, comprise from about 1% to about 10% (w / w) active ingredient, although the concentration of the active ingredient can be as high as the solubility limit of the active ingredient in the solvent. Formulations for topical administration may further comprise one or more of the additional ingredients described herein.A pharmaceutical composition described herein can be prepared, packaged, and / or sold in a formulation suitable for pulmonary administration via the buccal cavity. Such a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers, or from about 1 to about 6 nanometers. Such compositions are conveniently in the form of dry powders for administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and / or using a self-propelling solvent / powder dispensing container such as a device comprising the active ingredientdissolved and / or suspended in a low-boiling propellant in a sealed container. Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers. Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.Low boiling propellants generally include liquid propellants having a boiling point of below 65 °F at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w / w) of the composition, and the active ingredient may constitute 0.1 to 20% (w / w) of the composition. The propellant may further comprise additional ingredients such as a liquid non-ionic and / or solid anionic surfactant and / or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).Pharmaceutical compositions described herein formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and / or suspension. Such formulations can be prepared, packaged, and / or sold as aqueous and / or dilute alcoholic solutions and / or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and / or atomization device. Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and / or a preservative such as methylhydroxybenzoate. The droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition described herein. Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered by rapid inhalation through the nasal passage from a container of the powder held close to the nares.Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w / w) to as much as 100% (w / w) of the active ingredient, and may comprise one or more of the additional ingredients described herein. A pharmaceutical composition described herein can be prepared, packaged, and / or sold in a formulation for buccaladministration. Such formulations may, for example, be in the form of tablets and / or lozenges made using conventional methods, and may contain, for example, 0. 1 to 20% (w / w) active ingredient, the balance comprising an orally dissolvable and / or degradable composition and, optionally, one or more of the additional ingredients described herein. Alternately, formulations for buccal administration may comprise a powder and / or an aerosolized and / or atomized solution and / or suspension comprising the active ingredient. Such powdered, aerosolized, and / or aerosolized formulations, when dispersed, may have an average particle and / or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.A pharmaceutical composition described herein can be prepared, packaged, and / or sold in a formulation for ophthalmic administration. Such formulations may, for example, be in the form of eye drops including, for example, a 0. 1- 1.0% (w / w) solution and / or suspension of the active ingredient in an aqueous or oily liquid carrier or excipient. Such drops may further comprise buffering agents, salts, and / or one or more other of the additional ingredients described herein. Other ophthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and / or in a liposomal preparation. Ear drops and / or eye drops are also contemplated as being within the scope of this disclosure.Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and / or perform such modification with ordinary experimentation.Compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions described herein will be decided by a physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex,and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.The compounds and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and / or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and / or inhalation; and / or as an oral spray, nasal spray, and / or aerosol. Specifically contemplated routes are oral administration, intravenous administration (e.g., systemic intravenous injection), regional administration via blood and / or lymph supply, and / or direct administration to an affected site. Tn general, the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), and / or the condition of the subject (e.g., whether the subject is able to tolerate oral administration). In certain embodiments, the compound or pharmaceutical composition described herein is suitable for topical administration to the eye of a subject.The exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound, mode of administration, and the like. An effective amount may be included in a single dose (e.g., single oral dose) or multiple doses (e.g., multiple oral doses). In certain embodiments, when multiple doses are administered to a subject or applied to a biological sample (e.g., tissue, cell), any two doses of the multiple doses include different or substantially the same amounts of a compound described herein. In certain embodiments, when multiple doses are administered to a subject or applied to a biological sample (e.g., tissue, cell), the frequency of administering the multiple doses to the subject or applying the multiple doses to the biological sample (e.g., tissue, cell) is three doses a day, two doses a day, one dose a day, one dose every other day, one dose every third day, one dose every week, one dose every two weeks, one dose every three weeks, or one dose every four weeks. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the biological sample (e.g., tissue, cell) is one dose per day. In certainembodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the biological sample (e.g., tissue, cell) is two doses per day. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the biological sample (e.g., tissue, cell) is three doses per day. In certain embodiments, when multiple doses are administered to a subject or applied to a biological sample (e.g., tissue, cell), the duration between the first dose and last dose of the multiple doses is one day, two days, four days, one week, two weeks, three weeks, one month, two months, three months, four months, six months, nine months, one year, two years, three years, four years, five years, seven years, ten years, fifteen years, twenty years, or the lifetime of the subject, tissue, or cell. In certain embodiments, the duration between the first dose and last dose of the multiple doses is three months, six months, or one year. In certain embodiments, the duration between the first dose and last dose of the multiple doses is the lifetime of the subject, tissue, or cell. In certain embodiments, a dose (e.g., a single dose, or any dose of multiple doses) described herein includes independently between 0.1 pg and 1 pg, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg, between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg, between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and 300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 1 mg and 3 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 3 mg and 10 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 10 mg and 30 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 30 mg and 100 mg, inclusive, of a compound described herein.Dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.The compound or pharmaceutical composition thereof can be administered concurrently with, prior to, or subsequent to one or more additional pharmaceutical agents (e.g., a statin), which may be useful as, e.g., combination therapies. Pharmaceutical agents include therapeutically active agents. Pharmaceutical agents also include prophy tacticallyactive agents. Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved for human or veterinary use by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful for treating and / or preventing a disease (e.g., proliferative disease, inflammatory disease, autoimmune disease). Each additional pharmaceutical agent may be administered at a dose and / or on a time schedule determined for that pharmaceutical agent. The additional pharmaceutical agents may also be administered together with each other and / or with the compound or pharmaceutical composition thereof described herein in a single dose or administered separately in different doses. The particular combination to employ in a regimen will take into account compatibility of the compound described herein with the additional pharmaceutical agent(s) and / or the desired therapeutic and / or prophylactic effect to be achieved. In general, it is expected that the additional pharmaceutical agent(s) in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.The additional pharmaceutical agents include, but are not limited to, antiproliferative agents, anti-cancer agents, anti-angiogenesis agents, anti-inflammatory agents, immunosuppressants, anti-bacterial agents, anti-viral agents, cardiovascular agents, cholesterol-lowering agents, anti-obesity agents, anti-diabetic agents, anti-allergic agents, contraceptive agents, pain-relieving agents, probiotic, antibiotic, statin, or plasmid, and any combination thereof. In certain embodiments, the additional pharmaceutical agent is an antiobesity agent. In certain embodiments, the additional pharmaceutical agent is a probiotic. In certain embodiments, the additional pharmaceutical agent is an antibiotic. In certain embodiments, the additional pharmaceutical agent is a statin.In some embodiments, the additional pharmaceutical agent is an agent that increases the level of rhodoquinone in a subject. For example, the additional pharmaceutical agent can comprise a plasmid encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., RquA)), a viral vector (e.g., a viral vector encoding aprotein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., RquA)), and RNA encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., RquA)), a gene therapy (e.g., that activates synthesis of rhodoquinone or rhodoquinone intermediates), or a microbiome therapy (e.g., bacterial supplementation into the microbiome). In certain embodiments, the additional pharmaceutical agent is plasmid (e.g., a plasmid encoding RquA).Also provided herein are kits (e.g., pharmaceutical packs). In certain embodiments, a kit can comprise a compound (rhodoquinone mimetic) described herein.The kits provided may comprise a pharmaceutical composition or a compound (rhodoquinone mimetic) described herein and a container (e.g., a vial, ampule, bottle, syringe, and / or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of a pharmaceutical composition or compound described herein. In some embodiments, the pharmaceutical composition or compound described herein provided in the first container and the second container are combined to form one unit dosage form.Thus, in one aspect, provided are kits including a first container comprising a compound or pharmaceutical composition described herein. In certain embodiments, the kits are useful for treating a disease (e.g., a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder) in a subject in need thereof. In certain embodiments, the kits are useful for preventing a disease (e.g., a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder) in a subject in need thereof.In certain embodiments, a kit described herein further includes instructions for using the compound or pharmaceutical composition included in the kit. A kit described herein may also include information as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA). In certain embodiments, the information included in the kits is prescribing information. In certain embodiments, the kits and instructions provide for treating a disease (e.g., a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder) in a subject in need thereof. In certain embodiments,the kits and instructions provide for preventing a disease (e.g., a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder) in a subject in need thereof.In certain embodiments, a kit described herein includes a first container comprising a compound or pharmaceutical composition described herein. In certain embodiments, a kit described herein is useful in treating and / or preventing a disease, such as a metabolic disorder (e.g., obesity, diabetes), a hypoxia related disease (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder), or a disease resulting from rhodoquinone depletion (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, or neurodegenerative disorder).In certain embodiments, a kit described herein further includes instructions for using the compound or pharmaceutical composition included in the kit. A kit described herein may also include information as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA). In certain embodiments, the information included in the kits is prescribing information. In certain embodiments, the kits and instructions provide for treating a disease in a subject in need thereof, preventing a disease, such as a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder. A kit described herein may include one or more additional pharmaceutical agents described herein as a separate composition.Methods of UseProvided herein are methods of treating a disease (e.g., a metabolic disorder (e.g., obesity, diabetes), a hypoxia related disease (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder), or a disease resulting from rhodoquinone depletion (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, disease arising from alterations to the microbiome, or neurodegenerative disorder)) in a subject in need thereof. These methods can comprise administering to the subject a therapeutically effective amount of a compound (rhodoquinone mimetic) described herein.Also provided herein are methods of treating a disease (e.g., a metabolic disorder (e.g., obesity, diabetes), a hypoxia related disease (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder), or a disease resulting from rhodoquinone depletion (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, or neurodegenerative disorder)) in a subject in need thereof that comprise administering to the subject a therapeutically effective amount of a compound (rhodoquinone mimetic) described herein, wherein the subject has previously been administered a statin.Also provided herein are methods of treating a disease (e.g., a metabolic disorder (e.g., obesity, diabetes), a hypoxia related disease (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder), or a disease resulting from rhodoquinone depletion (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, or neurodegenerative disorder)) in a subject in need thereof that comprise administering to the subject a therapeutically effective amount of a compound (rhodoquinone mimetic) described herein in combination with a statin.Without wishing to be bound by any particular theory, statin treatment may lead to depletion of rhodoquinone in the subject, which may cause disease associated with depressed rhodoquinone levels (e.g., a proliferative disease, inflammatory disease, neuromuscular disorder, metabolic disorder, or neurodegenerative disorder).In certain embodiments, the disease is a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidative stress, or a mitochondrial DNA related disorder. In some embodiments a mitochondrial DNA disorder is characterized by one or more mutations in mitochondrial DNA. In certain embodiments, the disease is a proliferative disease. In certain embodiments, the disease is cancer. In certain embodiments, the cancer is associated with one or more mitochondrial mutations. In certain embodiments, the cancer is associated with one or more mitochondrial complex II mutations. In certain embodiments, the disease is a metabolic disorder. In certain embodiments, the disease is obesity.Without wishing to be bound by any particular theory, a compound (rhodoquinone mimetic) described herein may stimulate weight loss by forcing cells to bum fuels likeglucose and fatty acids more efficiently because rhodoquinone and / or rhodoquinol requires more fuel to be burned to generate energy in a subject.In certain embodiments, the disease is diabetes. In certain embodiments, the disease is an inflammatory disorder. In certain embodiments, the disease is autoimmune disease. In certain embodiments, the disease is a neuromuscular disorder. In certain embodiments, the disease is a neurodegenerative disorder. In certain embodiments, the disease is hypoxia. In certain embodiments, the hypoxia is caused by obesity. In certain embodiments, the hypoxia is caused by lower atmospheric oxygen content (e.g., at higher altitudes). In certain embodiments, the disease is mitophagy. In certain embodiments, the disease is ischemia. In certain embodiments, the disease is ischemia-reperfusion injury. In certain embodiments, the ischemia is ischemia of the heart. In certain embodiments, the ischemia is ischemia of the kidney. In certain embodiments, the ischemia is ischemia of the liver. In certain embodiments, the ischemia is caused by coronary artery disease. In certain embodiments, the ischemia is ischemia of the central nervous system. In certain embodiments, the ischemia is ischemia of the brain. In certain embodiments, the ischemia is caused by cardiomyopathy. In certain embodiments, the ischemia is caused by alcoholic cardiomyopathy. In certain embodiments, the ischemia is caused by angioplasty. In certain embodiments, the ischemia is caused by stenting. In certain embodiments, the ischemia is caused by a surgical procedure. In certain embodiments, the ischemia is caused by heart surgery such as bypass surgery or heart repair surgery (“open-heart surgery”). In certain embodiments, the ischemia is caused by organ transplantation. In certain embodiments, the ischemia is caused by prolonged weight pressure on tissues (pressure ulcers or bedsores). In certain embodiments, the ischemia is caused by ischemia-reperfusion injury which can cause damage to transplanted organs, tissues, or stem cells. In certain embodiments, the disease is oxidative stress. In certain embodiments, the oxidative stress is caused by elevated intracellular levels of reactive oxygen species (ROS). In certain embodiments, the oxidative stress is acetaminophen-induced. In certain embodiments, the disease is a mitochondrial DNA related disorder. In certain embodiments, the disease is CoQlO deficiency. In certain embodiments, the disease is mitochondrial complex 1 deficiency. In certain embodiments, the disease is mitochondrial complex 2 deficiency. In certain embodiments, the disease is mitochondrial complex 3 deficiency. In certain embodiments, the disease is mitochondrial complex 4 deficiency. In certain embodiments, the disease is mitochondrial complex 5 deficiency.In some embodiments, the compounds (rhodoquinone mimetics) described herein can be administered to a subject prophylactically, for example, during the ischemic event or after the ischemic event.In certain embodiments, provided herein are methods of inhibiting the Nrf2 pathway in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound (rhodoquinone mimetic) described herein.In certain embodiments, provided herein are methods of increasing AMPK activation in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound (rhodoquinone mimetic) described herein.In certain embodiments, the subject being treated is a mammal. In certain embodiments, the subject is a human. In certain embodiments, the subject is a domesticated animal, such as a dog, cat, cow, pig, horse, sheep, or goat. In certain embodiments, the subject is a companion animal, such as a dog or cat. In certain embodiments, the subject is a livestock animal, such as a cow, pig, horse, sheep, or goat. In certain embodiments, the subject is a zoo animal. In another embodiment, the subject is a research animal such as a rodent, dog, or non-human primate. In certain embodiments, the subject is a non-human transgenic animal, such as a transgenic mouse or transgenic pig.In certain embodiments, the biological sample being contacted with a compound (rhodoquinone mimetic) described herein, or pharmaceutical composition thereof, is breast tissue, bone marrow, lymph node, lymph tissue, spleen, or blood. In certain embodiments, the biological sample being contacted with the compound or pharmaceutical composition thereof is a tumor or cancerous tissue. In certain embodiments, the biological sample being contacted with the compound or pharmaceutical composition thereof is serum, cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from the biological sample.In certain embodiments, the cell or tissue being contacted with the compound or pharmaceutical composition thereof is present in vitro. In certain embodiments, the cell or tissue being contacted with the compound or pharmaceutical composition thereof is present in vivo. In certain embodiments, the cell or tissue being contacted with the compound or pharmaceutical composition thereof is present ex vivo. In certain embodiments, the skin is being contacted (e.g., the compound or pharmaceutical composition described herein isadministered topically to the skin, such as in a skin cream or cosmetic). In certain embodiments, the cell or tissue being contacted is a hypoxic cell or tissue. In certain embodiments, the cell or tissue being contacted is an ischemic cell or tissue. In certain embodiments, the cell or tissue being contacted with the compound or pharmaceutical composition thereof is a malignant cell (e.g., malignant blood cell). In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a malignant hematopoietic stem cell (e.g., malignant myeloid cell or malignant lymphoid cell). In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a malignant lymphocyte (e.g., malignant T-cell or malignant B-cell). In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a malignant white blood cell. In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a malignant neutrophil, malignant macrophage, or malignant plasma cell. In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a carcinoma cell. In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a breast carcinoma cell. In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a sarcoma cell. In certain embodiments, the cell being contacted with the compound or pharmaceutical composition thereof is a sarcoma cell from breast tissue. In certain embodiments, the biological sample is from tissue or cells with cancer (e.g., sarcoma, lung cancer, thyroid cancer, breast cancer, liver cancer, pancreatic cancer, gastric cancer, ovarian cancer, colon cancer, colorectal cancer, skin cancer, esophageal cancer; carcinoma). In certain embodiments, the biological sample is from tissue or cells with an inflammatory disease or autoimmune disease. In certain embodiments, the biological sample is from tissue or cells with cancer (e.g., sarcoma, lung cancer, thyroid cancer, breast cancer, liver cancer, pancreatic cancer, gastric cancer, ovarian cancer, colon cancer, colorectal cancer, skin cancer, esophageal cancer; carcinoma), an inflammatory disease, or an autoimmune disease.All types of biological samples described herein or known in the art are contemplated as being within the scope of the methods described herein. In certain embodiments, the disease (e.g., a proliferative disease, inflammatory disease, metabolic disorder, neuromuscular disorder, neurodegenerative disorder, hypoxia, ischemia, oxidativestress, or a mitochondrial DNA related disorder) to be treated or prevented using the compounds described herein is cancer.All types of cancers disclosed herein or known in the art are contemplated as being within the scope of the methods described herein. In certain embodiments, the proliferative disease is a hematological malignancy. In certain embodiments, the proliferative disease is a blood cancer. In certain embodiments, the proliferative disease is a hematological malignancy. In certain embodiments, the proliferative disease is leukemia. In certain embodiments, the proliferative disease is chronic lymphocytic leukemia (CLL). In certain embodiments, the proliferative disease is acute lymphoblastic leukemia (ALL). In certain embodiments, the proliferative disease is T-cell acute lymphoblastic leukemia (T-ALL). In certain embodiments, the proliferative disease is chronic myelogenous leukemia (CML). In certain embodiments, the proliferative disease is acute myeloid leukemia (AML). In certain embodiments, the proliferative disease is acute monocytic leukemia (AMoL). In certain embodiments, the proliferative disease is Waldenstrom’s macroglobulinemia. In certain embodiments, the proliferative disease is Waldenstrom’s macroglobulinemia associated with the MYD88 L265P somatic mutation. In certain embodiments, the proliferative disease is myelodysplastic syndrome (MDS). In certain embodiments, the proliferative disease is a carcinoma. In certain embodiments, the proliferative disease is lymphoma. In certain embodiments, the proliferative disease is T-cell lymphoma. In some embodiments, the proliferative disease is Burkitt’s lymphoma. In certain embodiments, the proliferative disease is a Hodgkin’ s lymphoma. In certain embodiments, the proliferative disease is a nonHodgkin’s lymphoma. In certain embodiments, the proliferative disease is multiple myeloma. In certain embodiments, the proliferative disease is melanoma. In certain embodiments, the proliferative disease is colorectal cancer. In certain embodiments, the proliferative disease is colon cancer. In certain embodiments, the proliferative disease is breast cancer. In certain embodiments, the proliferative disease is recurring breast cancer. In certain embodiments, the proliferative disease is mutant breast cancer. In certain embodiments, the proliferative disease is HER2+ breast cancer. In certain embodiments, the proliferative disease is HER2- breast cancer. In certain embodiments, the proliferative disease is triple-negative breast cancer (TNBC). In certain embodiments, the proliferative disease is a bone cancer. In certain embodiments, the proliferative disease is osteosarcoma. In certain embodiments, the proliferative disease is Ewing’s sarcoma. In some embodiments, the proliferative disease is a brain cancer. In some embodiments, theproliferative disease is neuroblastoma. In some embodiments, the proliferative disease is a cancer harboring mutations to the SDH complex. In some embodiments, the proliferative disease is renal cell carcinoma harboring mutations to the SDH complex. In some embodiments, the proliferative disease is a lung cancer. In some embodiments, the proliferative disease is small cell lung cancer (SCLC). In some embodiments, the proliferative disease is non-small cell lung cancer (NSCLC). In certain embodiments, the lung cancer is mesothelioma. In certain embodiments, the cancer is a thyroid cancer. In certain embodiments, the cancer is a sarcoma. In certain embodiments, the sarcoma is Kaposi’s sarcoma. In certain embodiments, the cancer is fallopian tube cancer. In certain embodiments, the cancer is a carcinoma. In certain embodiments, the carcinoma is fallopian tube carcinoma. In some embodiments, the proliferative disease is liver cancer. In some embodiments, the proliferative disease is prostate cancer. In some embodiments, the proliferative disease is pancreatic cancer. Tn some embodiments, the proliferative disease is gastric cancer. In some embodiments, the proliferative disease is ovarian cancer. In some embodiments, the proliferative disease is ovarian cancer. In some embodiments, the cancer is skin cancer. In some embodiments, the cancer is esophageal cancer. In some embodiments, the proliferative disease is a benign neoplasm. All types of benign neoplasms disclosed herein or known in the art are contemplated as being within the scope of the invention. In some embodiments, the proliferative disease is associated with angiogenesis. All types of angiogenesis disclosed herein or known in the art are contemplated as being within the scope of the invention. In certain embodiments, the cancer is a sarcoma, lung cancer, thyroid cancer, breast cancer, liver cancer, pancreatic cancer, gastric cancer, ovarian cancer, colon cancer, colorectal cancer, skin cancer, esophageal cancer; or a carcinoma.In certain embodiments, the disease is an inflammatory disease. In certain embodiments, the inflammatory disease to be treated or prevented using the compounds described herein is fibrosis (e.g., idiopathic pulmonary fibrosis, liver cirrhosis, cystic fibrosis, systemic sclerosis, progressive kidney disease, or cardiovascular fibrosis).In certain embodiments, the autoimmune disease to be treated or prevented using the compounds described herein is sclerosis (e.g., systemic sclerosis (scleroderma) or multiple sclerosis).In certain embodiments, the methods described herein include administering to a subject or contacting a biological sample with an effective amount of a compound (rhodoquinone mimetic) described herein or a pharmaceutical composition thereof. Incertain embodiments, the methods described herein include administering to a subject or contacting a biological sample with an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In certain embodiments, the compound is contacted with a biological sample. In certain embodiments, the compound is administered to a subject. In certain embodiments, the compound is administered in combination with one or more additional pharmaceutical agents described herein. The additional pharmaceutical agent may be an anti-proliferative agent. In certain embodiments, the additional pharmaceutical agent is an anti-cancer agent. In certain embodiments, the additional pharmaceutical agents include, but are not limited to, anti-proliferative agents, anti-cancer agents, anti-angiogenesis agents, anti-inflammatory agents, immunosuppressants, anti-bacterial agents, anti-viral agents, cardiovascular agents, cholesterol-lowering agents, anti-obesity agents, anti-diabetic agents, anti-allergic agents, contraceptive agents, pain-relieving agents, probiotic, antibiotic, statin, or plasmid (e.g., a plasmid encoding RquA), and any combination thereof. In certain embodiments, the additional pharmaceutical agent is an anti-obesity agent. In certain embodiments, the additional pharmaceutical agent is a probiotic. In certain embodiments, the additional pharmaceutical agent is an antibiotic. In certain embodiments, the additional pharmaceutical agent is a statin.In some embodiments, the additional pharmaceutical agent is an agent that increases the level of rhodoquinone in a subject. For example, the additional pharmaceutical agent can comprise a plasmid encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., a mitochondrially targeted RquA)), a viral vector (e.g., a viral vector encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., a mitochondrially targeted RquA)), and RNA encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., a mitochondrially targeted RquA)), a gene therapy (e.g., that activates synthesis of rhodoquinone or rhodoquinone intermediates), or a microbiome therapy (e.g., bacterial supplementation into the microbiome). In certain embodiments, the additional pharmaceutical agent is plasmid (e.g., a plasmid encoding a mitochondrially targeted RquA).In some embodiments, the additional pharmaceutical agent is an anti-obesity agent. In some embodiments, the additional pharmaceutical agent is a probiotic. In some embodiments, the additional pharmaceutical agent is an antibiotic. In some embodiments,the additional pharmaceutical agent is a statin. In some embodiments, the additional pharmaceutical agent is a plasmid (e.g., a plasmid encoding a mitochondrially targeted RquA). In certain embodiments, a pharmaceutical composition described herein further comprises a combination of the additional pharmaceutical agents described herein.Also provided herein are methods of reducing oxidation and / or oxidative stress in a biological sample that comprise contacting the biological sample with a compound (rhodoquinone mimetic) described herein.Also provided herein are methods for reducing or preventing oxidation in a composition that comprise contacting the composition with a compound (rhodoquinone mimetic) described herein. In certain embodiments, the composition can comprise a food, skin cream, a nutrient, a chemical, a pharmaceutical agent, a polymer, a biological sample, a protein, or a nucleic acid.Also provided herein are methods of using the compounds (rhodoquinone mimetics) described herein as antioxidants or preservatives, as nutritional supplements, and ex vivo to prevent oxidative and / or oxidative stress in a biological sample, such as blood, tissue, skin, and / organs in storage and / or blood, tissue, and / organs before and / or during transplantation.EXAMPLESThe invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of non- critical parameters which can be changed or modified to yield essentially the same results. Example 1. Rhodoquinone is an Electron Carrier in the Mammalian Electron Transport ChainSummaryUbiquinone (UQ), the only known electron carrier in the mammalian electron transport chain (ETC), preferentially delivers electrons to the terminal electron acceptor oxygen (O2). In hypoxia, ubiquinol (UQH2) diverts these electrons onto fumarate instead. In this Example, we describe rhodoquinone (RQ), an electron carrier detected in mitochondria purified from certain mouse and human tissues, that preferentially delivers electrons to fumarate through reversal of succinate dehydrogenase, independently of environmental O2 levels. The RQ / fumarate ETC is strictly present in vivo and is undetectable in cultured mammalian cells. Using genetic and pharmacologic tools that reprogram the ETC from theUQ / O to the RQ / fumarate pathway, we establish that these distinct ETCs support unique programs of mitochondrial function, and that RQ confers protection upon hypoxia exposure in vitro and in vivo. Thus, in discovering the presence of RQ in mammals, we unveil a tractable therapeutic strategy that exploits flexibility in the ETC to ameliorate hypoxia- related conditions.IntroductionMammalian mitochondria serve multifaceted roles in metabolism that require flow of electrons through the electron transport chain (ETC). The ETC is comprised of reduction and oxidation (redox) reactions whereby electron donors transfer electrons to ubiquinone (UQ), ultimately landing on fumarate or oxygen (O2) as the electron acceptor. Redox reactions liberate free energy that is harnessed to facilitate proton pumping and mitochondrial functions including ATP and de novo pyrimidine synthesis, proline catabolism, and hydrogen sulfide detoxification.The Nernst equation dictates the free energy released by redox reactions. In standard conditions (1 M concentrations, 25°C, and 0.1 MPa), the difference in the standard reduction potential (E 0) of the electron donor and acceptor dictates thermodynamic favorability (AG° = -nFAE 0). Reactions are favorable when the metabolite receiving electrons has a higher E 0 than the metabolite donating them. In physiological conditions, factors including temperature, pH, and the ratio of reduced to oxidized forms, impact the thermodynamic favorability (AG = AG° + RT InQ). Embedding molecules in membranes, such as the ETC, alters their redox properties; for instance, the E oof UQ shifts from +100 mV in an aqueous solution to +234 mV in a lipid monolayer. Redox reactions catalyzed by Complex I (NADH oxidation and UQ reduction), Complex III (ubiquinol (UQH2) oxidation and cytochrome C reduction), and Complex IV (oxidation of cytochrome C and reduction of O2), are extremely favorable due to their large AE°, releasing sufficient free energy to facilitate proton pumping.Succinate dehydrogenase (SDH, also known as Complex II) is unique as it is reversible in physiological contexts and doesn’t pump protons. Given the higher E 0 of UQ / UQH2 compared to succinate / fumarate, SDH favors the forward, succinate oxidase, activity. However, the AE 0 between UQ / UQH2 and succinate / fumarate is low enough (+70 mV, compared to +420 mV for NAD / NADH and UQ / UQH2) to allow environmental conditions dictate the net-directionality of the reaction. In hypoxia, UQH2 accumulates,leading to SDH reversal and fumarate reduction. Without ETC inhibition, SDH reversal requires an alternative electron carrier that has a lower E° than fumarate. Although UQ is the only known mammalian electron carrier, the reverse, fumarate reductase reaction occurs in physiological conditions. Theoretically, this is thermodynamically unfavorable, inspiring us to investigate the mechanism underlying this phenomenon.Materials and MethodsCell lines: A total of 5 cell lines were used in this work. The 143B, Caki-1, DLD1, HEK293T and HCT116 cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher) supplemented with 10% Heat Inactivated Fetal Bovine Serum (ThermoFisher), 1% penicillin and streptomycin (ThermoFisher), and 100 pg / mL uridine (Sigma). RquA expression was induced using 250 ng / mL doxycycline. Cells were kept in a 37°C incubator (Baker Ruskinn) held at 5% CO2 and 90% relative humidity. To passage and seed cells, adherent cells were washed with IX PBS (Gibco), incubated with 0.25% Trypsin (Gibco) in a 37°C incubator, harvested, and pelleted by centrifugation. Supplements: Antimycin A (Sigma), Rotenone (Sigma), Doxycycline (Takara). Cell lines were authenticated and tested negative for mycoplasma.Animals: 8-16- week-old male and female wild-type C57BL / 6J mice (RRID:IMSR_JAX:000664) acquired from the Jackson Laboratory were used for these studies. Animals were housed in the UMCMS Animal Facility and maintained according to the Spinelli Lab protocol (PRGT0202200067). All protocols related to mouse work were approved by the Institutional Animal Care and Use Committee (IACUC) and the Institutional Biosafety Committee (IBC) at the University of Massachusetts Chan Medical School (UMCMS). Up to 5 total mice per cage were housed together and all animals in the study were healthy and wild-type prior to perturbations described.Hypoxia Cell Culture: For experiments done in hypoxia, cells were initially seeded in normoxia (as described above). 24 hours after seeding, the cells are transferred into the Invivo2 1000 workstation (Baker Ruskinn) with the oxygen tension set to 0.5% O2, the temperature to 37°C, the CO2 to 5%, and the relative humidity to 80%.Generation of Stable Cell Lines: RquA cDNA was codon optimized for expression in human cells and cloned into the pCW57.1 -Luciferase backbone (Addgene 9928). The RquA and SDHB KO (Addgene 177981) plasmids were co-transfected into HEK293T cells with lentiviral packaging particles. The relevant cell lines were infected with the lentivirusand selected with puromycin, generating stable knockout or RquA-expressing cell lines. All plasmids were sequenced and verified (Psomagen).Proliferation: 25,000 - 50,000 cells were seeded in complete DMEM media. 24 hours later the media was changed to reflect the relevant treatments. The cells were incubated for 5-7 days to proliferate and every 2 days the media was refreshed with the relevant treatments. Once the desired number of days were reached, the cells were washed with IX PBS, trypsinized, and then quenched with complete DMEM media. Cells were resuspended to break up clumps and transferred to coulter counter cups (Beckman) filled with isotone buffer (Beckman 8546719). Cells were counted on a Beckman Coulter Counter (Beckman).H2O2 measurements: Cells were seeded 1 week prior to experimentation to adapt to the relevant oxygen conditions. On the day of experiment, media was refreshed with the relevant conditions and cells were incubated for 30 minutes in the tissue culture incubator. After 30 minutes of incubation, cells were treated with 1.25 p M CellROX orange dye (Invitrogen) and incubated for 30 minutes. 1.25 mM N-Acetyl Cysteine (Sigma) and 100 pM Tert-butyl hydroperoxide (Sigma) were used as controls. After incubation, cells were washed with PBS, trypsinized, and transferred to a new 1.5 mL tube. The cells were then pelleted at 1,000 x g, the media was aspirated, and the pellets were resuspended in lx PBS to 2 million cells per mL. The fluorescence intensity of the dye was measured on the LSR-II sorter (BD Biosciences), excited with the 561 nm laser, and analyzed in the PE channel.Mitochondrial Membrane Potential: Cells were seeded in DMEM containing 10% FBS, 1% penicillin and streptomycin, and 0.1 mg / mL uridine (Sigma) in 12-well dishes. 24 hours prior to FACS, the media was changed and the respective compounds were added. Cells were incubated for 30 minutes in a tissue culture incubator with 100 nM Tetramethylrhodamine, Ethyl Ester (TMRE) (invotrogen). After incubation, cells were washed with PBS, trypsinized, and transferred to a 1 .5 mL tube. The cells were then pelleted at 1,000 x g, the media was aspirated, and the pellets were resuspended in lx PBS. The fluorescence intensity of the dye was measured on the LSR-II sorter (BD Biosciences), excited with the 561 nm laser, and analyzed in the PE channel.Immunofluorescence: 75,000 wild-type and RquA-expressing 143B cells were seeded in 2- well chamber slides (ThermoScientific) with 100 ng / mL doxycycline. Cells were fixed 40 hours after seeding with 4% paraformaldehyde for 10 minutes at room temperature. Then, cells were blocked and permeabilized in 0.3% TritonX-100, 5% donkeyserum in PBS for 30 minutes and incubated for 1 hour at room temperature with primary antibodies against COX4 (Cell Signaling Technology) and FLAG (Cell Signaling Technology) at 1 :250 and 1:500 respectively, diluted in 0.3% TritonX-100, 5% donkey serum in PBS. Secondary antibodies Alexa Fluor 488 goat- anti-rabbit (abeam) and Alexa Fluor 647 goat-anti-mouse (abeam) were diluted to 1 :333 in 0.3% TritonX-100, 5% donkey serum in PBS and incubated for 45 minutes at room temperature in the dark. Chamber slides were mounted using ProLong Gold Glass + NucBlue (ThermoFisher). After over 24 hours, slides were imaged on a Zeiss LSM 900 confocal microscope at 63x magnification (Zeiss).NMR Analysis of HKJS001 and HKJS003: HKJS001 and HKJS003 were synthesized as described below and NMR analysis was performed to confirm structures. Briefly, 'H-NMR analysis of HKJS001 and HKJS003 was performed in sample resuspended in DMSO-d6and acquired at 400 MHz.13C-NMR analysis of HKJS001 and HKJS003 was performed in sample resuspended in DMSO-t / 6and acquired at 100 MHz.Western Blots: The cells were lysed in a 1 :10 dilution of lOx RIPA Lysis Buffer (Sigma) supplemented with complete EDTA-free protease inhibitor (Sigma) and clarified by centrifugation. Protein content was quantified using a Pierce BCA Protein Assay Kit (Life Technologies) and 20 pg protein were loaded on a 4-20% Tris-Glycine Novex Gels (Invitrogen). Proteins were subsequently transferred to a 0.45 mm PVDF membrane (Sigma). Primary antibodies were used at the following dilutions in 5% BSA: Total OXPHOS Rodent WB Antibody Cocktail- containing NDUFB8, SDHB-30kDa, UQCRC2, MT-CO1, and CV alpha subunit (Abeam; 1: 1000), FLAG (Cell Signaling Technology; 1:1000), HIFla (Cell Signaling Technology; 1:1000), TOMM20 (Santa Cruz Biotechnology; 1:1000), GLUT1 (Abeam; 1 :1000), and Actin (Cell Signaling Technology; 1: 1000). Secondary antibodies were used at the following dilutions in 5% Milk: Anti-rabbit IgG HRP-linked Antibody (1 :5000, Cell Signaling Technology), Anti- mouse IgG HRP- linked Antibody (1 :5000, Cell Signaling Technology). Blots were developed using SignalFire ECL Reagent (Cell Signaling Technology) and exposed using autoradiography film.BN-PAGE: 50 pg of isolated mitochondria were lysed in 20 pl NativePAGE™ lx sample buffer (Thermo BN2008), containing 2 % digitonin for 20 min on ice. Mitochondrial lysates were centrifuged at 20000 g for 20 min at 4 °C, the supernatant was mixed with NativePAGE™ G-250 sample additive (0.25 % detergent concentration) loaded onto NativePAGE™ 3-12 %, Bis-Tris gels (Thermo BN1001) and run according tomanufacturer’s instructions (Thermo BN2007). Proteins were transferred onto a 0.45 mm PVDF (Sigma) membrane using lx NuPAGE™ transfer buffer (Thermo NP0006), and subsequently probed for NDUFS1 (Cell Signaling 60153S), SDHA (ProteinTech 14865-1 - AP), CYC1 (ProteinTech 10242-1-AP), COX4 (Cell Signaling 4850S) and ATP5A1 (Cell Signaling 18023S).Isolation of mitochondria from cells and tissues: To isolate mitochondria, cells were pelleted at 1000 x g for 5 minutes and washed with IX PBS. Cell pellets could be stored at -80 °C until the mitochondria were isolated. Tissues were first powderized with a mortar and pestle in liquid nitrogen and 50 mg was aliquoted for mitochondrial isolation. The pelleted cells or tissue powder was resuspended in 2 ml of ice-cold isolation buffer (0.22 M Mannitol, 0.075 M Sucrose, 1 mM EDTA, 10 mM HEPES pH 7.4, and one complete Protease inhibitor tablet) and transferred into an ice-cold homogenizer. The samples were dounced in a PTFE tissue grinder (VWR) 30 times and transferred into a new 2 ml Eppendorf tube. Samples were centrifuged at 600 x g for 10 minutes at 4 °C and the supernatant was transferred to a new tube. Samples were centrifuged at 7,000 x g for 10 minutes at 4 °C and the supernatant was discarded. Pellets were washed with 1 mL of isolation buffer and pelleted at 7,000 x g for 10 minutes at 4 °C. The supernatant was discarded and the samples were stored in -80 °C until they were ready for use in the assay. On the day of the assay, mitochondria pellets were taken out of the -80 °C freezer and thawed for 1 hour on ice.Quantification of protein in mitochondria pellets: The pellets were resuspended in 1 mL isolation buffer (0.22 M Mannitol, 0.075 M Sucrose, 1 mM EDTA, 10 mM HEPES pH 7.4, and one cOmplete Protease inhibitor tablet) with a pipettor. 25 pL was aliquoted aside to later be used for protein quantification. Samples were centrifuged at 7,000 x g for 10 minutes at 4 ° C and the supernatant was discarded. The 25 pL aliquot of mitochondria was resuspended in 250 pL of 1 :10 dilution of lOx RIPA Lysis Buffer (0.5M Tris-HCl, pH 7.4, 1.5M NaCl, 2.5% deoxycholic acid, 10% NP-40, lOmM EDTA (Sigma), cOmplete EDTA-free protease inhibitor (Sigma)), vortexed for 10 minutes at 4° C, and clarified by centrifugation at 4° C. Protein content was quantified using a Pierce BCA Protein Assay Kit (Life Technologies).Permeabilize mitochondria for SDH activity assay: Mitochondria pellets were resuspended to 5 mg / mL in Mito isolation buffer (0.22 M Mannitol, 0.075 M Sucrose, 1 mM EDTA, 10 mM HEPES pH 7.4, and one cOmplete Protease inhibitor tablet). Thesamples were freeze-thawed 5 times using a -80 °C freezer. The samples were kept on ice during the preparation for the assay.SDH activity assay: Base assay buffer containing 27.5 mM KH2PO4 (Sigma) pH 7.4 (pH using KOH), 1 mM K-ADP (Sigma), and 12.5 mM Fumaric Acid (Sigma) was made. 5 mg / mL permeabilized mitochondria were diluted in base assay buffer to a final concentration of 0.7 mg / mL. The permeabilized mitochondria and base assay buffer were aliquoted into tubes and prewarmed in a 37 °C water bath for 10 minutes. Reactions were initiated by adding NADH to a final concentration of 10 mM (a 100 mM NADH stock resuspended in 27.5 mM KH2PO4 pH 9.0 was made). The sample was mixed by pipetting up and down with a p200 pipette and immediately the tubes were placed in the 37 degree water bath for the appropriate amount of time. The samples were quenched with 500 p L of 80% LC-MS grade MeOH (Sigma), 20% LC-MS grade water (Sigma). The samples were vortexed for 10 minutes at 4°C and centrifuged at 16,000 x g for 10 minutes at 4 °C. The supernatant was moved into new Eppendorf tubes, dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator (Labconco) connected to a CentriVap- 105 Cold Trap (Labconco), and stored in the -80 °C until they were ready to be analyzed on the LC-MS. Metabolite pellets were re-suspended in 200 uL of LC-MS grade water (Sigma) and vortexed for 10 minutes at 4 °C. Samples were centrifuged at 16,000 x g for 10 minutes at 4 °C and supernatant was moved into LC-MS vials.Oxygen Consumption Rate (Seahorse): Respiration was measured on the Seahorse XFe-96 Analyzer (Seahorse Bioscience). Cells were incubated in a non-CCL 37°C incubator in serum-free Seahorse XF RPMI Media (Seahorse Bioscience, Catalog # 103336) supplemented with 5 mM glucose, 2 mM glutamine, and 1 mM pyruvate. Oxygen consumption rate (OCR) was measured over a period of 30 minutes. 500 nM antimycin A was injected into wells to control for ETC-dependent oxygen consumption.Molecular Docking: 3D protein structures were obtained from the RCSB Protein Data Bank (PDB): 5XTD, 8GS8. To prepare the protein structures for docking, water molecules, and ligands were removed, and polar hydrogens were added using AutoDockTools (Version 1.5.7). Ligand structures were prepared using Avogadro (Version 1.2). Docking search spaces were defined using PyRx (Version 0.8). For Complex 1, a docking search space was defined with dimensions 20 x 10 x 25 A centered on the UQ binding site. For Complex II, a docking search space was defined with dimensions 35 x 20 x 20 A centered on the UQ binding site. Molecular docking and free energy calculations wereperformed using AutoDock Vina (Version 1.1.2), with an exhaustiveness parameter of 16. 3D Docking visualizations were generated using PyMol (Version 3.0.3, Schrodinger, LLC.).RNA Sequencing: A total of 5 x 105cells from each cell line were plated in 10 cm plates and grown for 144 h. Cells were provided fresh media 3 h before collecting. Media was aspirated and cells were immediately lysed in dishes and total RNA was purified using Qiagen RNeasy kits. A quantity of 1 pg of total RNA was used for mRNA purification with the NEBNext Poly(A) mRNA Magnetic Isolation Module (cat# E7490L). NEBNext Ultra II Directional RNA Library Prep Kit with Sample Purification Beads (cat# E7765L) were used for RNA-seq library preparation. NEBNext Multiplex Oligos for Illumina (cat# E6440S) were used for indexing during PCR amplification of the final libraries. Libraries were quantified by qPCR using the NEBNext Library Quant Kit for Illumina (cat# E7630S) and multiplexed accordingly. Samples were sequenced (single-end) on a P2 100 cycle kit (cat# 2004681 1 ) from Illumina on the NextSeq2000 platform, and fastq files were generated using the BCL convert (version 3.8.2) software from Illumina. Sequences were aligned to the human reference genome hgl9 using bwa (version 0.7.17) default settings, and bam files were sorted using samtools (version 1.16.1). Aligned reads to gene transcripts were counted using the subread feature Counts function (version 1.6.2) with default settings. Gene- level counts were converted to RPKM (reads per kilobase per million reads) and edgeR (version 3.36.0) was utilized for differential expression analysis between groups, followed by gene set enrichment analysis with fgsea (version 1.20.0) using the Hallmarks gene sets.Mouse Experiments: C57 BL / 6 mice were used for the following studies. In vivo stable isotope tracing experiments were performed by tail vein and intraperitoneal bolus injections of13Cs15N2-glutamine dissolved in IX PBS. 0.2 g / kg was injected into the tailvein and 0.75 g / kg was injected intraperitoneally. For experiments involving HKJS001 injections, 6.5 mg / kg was injected intraperitoneally and an equivalent amount of DMSO was used in control mice. Mice were euthanized 45 minutes after the injections. Tissues were harvested, flash frozen in liquid nitrogen, and stored at -80°C until samples were ready for processing.For ischemia reperfusion injury studies, mice at 8-12 weeks of age were anesthetized via intraperitoneal injection with a combination of 100 mg / kg ketamine hydrochloride and 5 mg / kg xylazine (Webster Veterinary, Devens, MA) before surgery. Unilateral hindlimb ischemia in the right leg was introduced following an established protocol. Hindlimb tissue perfusion was assessed with a moorLDI2-IR laser Dopplerimaging system (Moor Instruments, Devon, UK). Blood flow images were obtained under conditions of constant body temperature (36 ± 1.0 °C) and average hindlimb blood flow was expressed as the ratio of ischemic to non-ischemic foot flow to account for minor variations in imaging conditions.Adeno- associated viruses (AAVs) were used as approved on the Spinelli Lab IBC protocol (#1-839-22). Briefly, rAAV was produced by transient HEK 293 cell transfection and CsCl sedimentation by the University of Massachusetts Medical School Viral Vector Core. Vector genome titers of the rAAV preparations for control virus (AAV9.Tre3G- mCherry SV40 CB6 Tet-on 3G RBG) and RquA virus AAV9.Tre3G-RquA SV40 CB6 Teton 3G RBG were determined by ddPCR, and purity was assessed by 4%-12% SDS- acrylamide gel electrophoresis and silver staining (Invitrogen). Mice were intravenously injected with 6 X 10A11 genome copies of either virus and given 1 mg / mL doxycycline in the drinking water for 7 days to induce either mCherry or RquA expression.Primary Hepatocyte Isolation and Culture: First, 10-week-old male C57BL6 / J mice on a chow diet were sacrificed using CO2. Quickly after, the inferior vena cava was cannulated using an IV catheter, and liver perfusion was performed with Perfusion Buffer (HBSS without Ca2+, Mg2+with 0.5 mM EDTA) to wash out blood and chelate calcium within the tissue. The portal vein was cut to allow perfusion. Digestion Buffer (HBSS with Ca2+, Mg2+and 1 mg / mL liberase) was then perfused into the liver to break down the extracellular matrix and fully dissociate the liver cells. The digested livers were transferred to a petri dish and minced in 10 mL HBSS with Ca2+and Mg2+, and filtered using a 100 pm cell strainer into 50 ml sterile conical tubes.After centrifuging the digested livers for 3 minutes at 50xg at 4°C, primary hepatocytes were obtained in the pellet. The pellet was washed three times with HBSS and resuspended in 40 ml Plating Media (DMEM low glucose, 5% FBS, 1% P / S). Hepatocytes were then plated in 6-well plates at a density of 500,000 cells per well. Three hours postplating, cell adherence was confirmed under a microscope, and the media was changed to Maintenance Media (Medium 199 1% P / S). Cells were harvested at Day 1, Day 2, and Day 3 post-plating for further analysis.Human tissue experiments: De-identified post-mortem human tissues were acquired from the University of Massachusetts Chan Medical School Biorepository and Tissue Bank and their use was approved under the Spinelli lab IBC protocol #1-839-22. Tissue samples were powderized and extracted for metabolites as described below.Metabolomics AssaysSuperoxide measurement: Cells were seeded in a 6- well plate and a duplicate for each plate was also seeded for cell count normalization. Cells were seeded in complete DMEM containing 10% FBS, 1% P / S, and 0.1 mg / mL uridine. Plates were moved to their conditional oxygen levels the next day and allowed to adapt for at least 72 hours. On the day of the experiment, 1 p M MitoSox Red (Thermo Scientific) was added to each well and then the wells were incubated for 30 minutes. MitoSox and 2-hydroxyethidium (the oxidation product of MitoSox) were then isolated. Media was aspirated, wells were washed twice with 1 mL of PBS, and then plates were then moved onto dry ice. 800 p L of HPLC- grade isopropanol (Sigma) was added and plates were moved into a -80°C freezer for 15 minutes and then scraped with a cell scraper. Lysates were transferred to 1.5 mL Eppendorf tube, vortexed for 10 minutes in a 4°C cold room, and then centrifuged for 10 minutes at 21 ,300 x g at 4°C. 200 pL of supernatant was transferred to a newly labeled 1 .5 mL Eppendorf tube and dried in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap- 105 Cold Trap (Labconco). Samples were resuspended with 100 pL of 3:3:1 (HPLC-grade methanol (Sigma): HPLC -grade chloroform (Sigma): HPLC- grade water (Sigma)) solution and vortexed for 10 minutes at 4°C. Samples were moved into LCMS vials and run on the MitoSox LC-MS method.Polar metabolite isolation from cultured cells: Media was aspirated from the plates and then the cells were washed with lx PBS twice. The plate was then transferred to dry ice and 500 pL of 80% HPLC-grade methanol (Sigma) 20% HPLC-grade water (Sigma) was added to each well. The wells were placed in a -80 freezer to incubate for 15 minutes. The plates are taken out of the freezer one at a time and placed back on dry ice. The cells were then scraped and transferred to a new tube. Each well was washed with an additional 300 pL of 80% HPLC-grade methanol (Sigma) 20% HPLC-grade water (Sigma) and collected into the same tube as the initial lysis. The samples were then vortexed at 4° C for 10 minutes and centrifuged at 21,300 x g for 10 minutes at 4° C. Supernatants were transferred to a new tube and dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap (Labconco). After being dried down, pellets were stored in a -20° C freezer until ready to run on the polar LC-MS method.13Cs15N2-glutamine tracing in vitro". Cells were seeded in complete DMEM 48 hours prior to tracing so that wells reached 75% confluence at the time of the experiment. 24 hours after seeding, cells were treated with their respective conditions and incubated forthe indicated times. For experiments involving the hypoxia chamber, media were preconditioned at the relevant O2 levels for 72 hours prior to use for experiments. Tracing media was then prepared, with glutamine-free DMEM (Gibco) containing 10% FBS, 1% P / S, and 0.1 mg / mL uridine supplemented with 2 mM13C515N2-glutamine (Cambridge Isotope Labs). Media was refreshed in each well with stable isotope tracing media and incubated for 8 hours. Polar metabolites were then isolated as described above and ran on the polar LC-MS method.13C4-aspartate tracing in vitro". Cells were seeded in complete DMEM 96 hours prior to tracing so that wells reached 75% confluence at time of experiment. DMEM containing 10% FBS, 1% penicillin and streptomycin, and 0.1 mg / mL uridine (Sigma) was used when seeding the experiment. 72 hours prior, the media was changed to DMEM containing 10% FBS, 1% penicillin and streptomycin, and 10 mM aspartate with the pH adjusted to 7.4 along with the relevant treatments. 6 hours prior to metabolite isolation, the cells were treated with DMEM containing 10% FBS, 1% penicillin and streptomycin, and 10 mM13C4-aspartate (Sigma) and the pH adjusted to 7.4 with the relevant treatments. After the 6-hour incubation period, polar metabolites were then isolated as described above and ran on the polar LC-MS method.UQ / RQ isolation from cultured cells: Plates were removed from incubator, media was aspirated, wells were washed with IX PBS, and the wash was aspirated. Plates were moved to dry ice and 500 pL of 100% LCMS-grade ethanol (Sigma) was added to each well. Cells were then scraped with cell scraper and lysate was moved to a labeled and precooled 1.5 mL Eppendorf tube. Samples were then vortexed for 10 minutes in a cold room. Then, 1 mL of 100% LCMS-grade hexane (sigma) added to it and samples were vortexed for another 10 minutes in the cold room. Samples were centrifuged for 10 minutes at 21,300 x g at 4°C. The top (hexane) layer of the sample (containing UQ and RQ) was transferred to a new labeled 1.5 mL Eppendorf tube and dried in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap (Labconco). Samples were stored in -80°C freezer prior to resuspension and running on LC-MS.13Cs15N2-glutamine tracing in vivo:13C515N2-glutamine (Cambridge Isotope labs) was resuspended to 50 mg / mL in IX PBS. C57BL / 6 mice between the ages of 10-16 weeks were weighed to allow injection of 0.75 g / kg intraperitoneally and 0.2 g / kg intravenously via the tail vein. Mice were injected with the respective amounts of13Cs15N2-glutamine, were sacrificed after 45 minutes, and tissues were harvested and flash frozen in LiquidNitrogen. Samples were stored at -80°C until their extraction and run on the polar LC-MS method.Polar metabolite isolation from tissues: Tissues were flash frozen in liquid nitrogen and powderized using a mortar and pestle. Approximately 10 mg of tissue powder was transferred into an Eppendorf tube. The tissue powder was re-suspended in 800 pL precooled HPLC-grade 60:40 Methanol: Water (Sigma) and then vortexed for 15 minutes at 4°C. 500 pL of pre-cooled LC-MS grade chloroform (Sigma) was added to the lysate and again vortexed for 15 minutes at 4°C. Samples were then centrifuged at 16,000 x g for 10 minutes at 4°C, creating three layers: the top layer containing polar metabolites, the middle layer containing protein, and the bottom layer containing non-polar metabolites. The top layer was transferred into a new Eppendorf tube, dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap- 105 Cold Trap (Labconco), and stored at -80°C until they were re-suspended for LC-MS analysis. The non-polar layer was discarded, and the remaining protein layer was saved for protein quantification. The protein layer from the metabolite isolation was re-suspended in 1 mL of RIPA buffer (150 mM NaCl, 50 mM Tris HC1 pH 7.5, 0.1% SDS, 1% Triton-X 100 (Sigma), 0.5% deoxycholate (Sigma), cOmplete EDTA-free protease inhibitor (Sigma)). The samples were vortexed for 10 minutes at 4°C and then centrifuged at 16,000 x g for 10 minutes at 4°C. Protein concentrations for each sample were calculated using the Pierce BCA Protein Assay Kit (Life Technologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (1 pg / pL) concentration.Isolation of HKJS001 from liver: Tissues were flash frozen and powderized with a mortar and pestle in a liquid nitrogen bath. Approximately 10-20 mg of tissue powder was transferred into Eppendorf tubes and re-suspended in 500 pL pre-cooled HPLC-grade Ethanol (Sigma). Samples were vortexed for 10 minutes at 4 °C. Then, 1 mL of pre-cooled HPLC-grade hexane (Honeywell) was added to the lysate and samples were vortexed for an additional 10 minutes at 4 °C. Samples were centrifuged at 16,000 x g for 10 minutes at 4 °C, creating two layers - the top hexane layer and bottom ethanol layer. The top (hexane) fraction was moved into a new tube and dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap- 105 Cold Trap (Labconco), and subsequently stored at -80°C until they were analyzed by LC-MS. Metabolite pellets were re-suspended in HPLC-grade 80:20 EtOH:Hexane (Sigma) and vortexed for 10 minutes at 40C. Samples were centrifuged at 16,000 x g for 10 minutes at 40C and supernatant was moved into LC-MS vials. Samples were run on the HKJS-001 LC-MS method.UQRQ isolation from tissues: Tissues were flash frozen in liquid nitrogen and powderized using a mortar and pestle. Approximately 10 mg of tissue powder was transferred into an Eppendorf tube. The tissue powder was re-suspended in 500 pL of 99.9% LCMS-grade methanol (Fisher) 0.1% HC1 and then vortexed for 15 minutes at 4°C. 500 pL LCMS-grade hexane (Honeywell) was added to the lysate and again vortexed for 15 minutes at 4°C. Samples were then centrifuged at 16,000 x g for 10 minutes at 4°C with the top (hexane) layer containing UQ and RQ, the middle layer containing the acidified methanol, and the bottom layer containing the protein. The top layer was transferred into a new Eppendorf tube, dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap- 105 Cold Trap (Labconco), and stored at -80°C until they were re-suspended for LC-MS analysis. The acidified methanol layer was discarded, and the bottom protein layer was saved for protein quantification. The protein layer from the metabolite isolation was re-suspended in 1 mL of RIPA buffer (150 mM NaCl, 50 mM Tris HC1 pH 7.5, 0.1% SDS, 1% Triton-X 100 (Sigma), 0.5% deoxycholate (Sigma), cOmplete EDTA-free protease inhibitor (Sigma)). The samples were vortexed for 10 minutes at 4°C and then centrifuged at 16,000 x g for 10 minutes at 4°C. Protein concentrations for each sample were calculated using the Pierce BCA Protein Assay Kit (Life Technologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (20 pg / pL) concentration.Isolation of UQ / RQ from purified mitochondria: Mitochondria purification was performed as described above in the section on isolating mitochondria for biochemical assays. Purified mitochondria pellets were subsequently vortexed in 500 pL of 99.9% LCMS-grade methanol (Fisher) 0.1% HC1 for 10 minutes at 4°C. 500 pL of 100% LCMS- grade hexane (Honeywell) was added to each tube and vortexed for an additional 10 minutes at 4°C. Samples were then centrifuged for 10 minutes at 21,300 x g at 4°C. The top (hexane) layer of the sample (containing UQ and RQ) was transferred to a new labeled 1.5 mL Eppendorf tube and dried in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap- 105 Cold Trap (Labconco). Samples were stored in -80°C freezer prior to resuspension and running on LC-MS. The bottom layer was discarded and the pellet was saved for protein quantification. Protein was isolated as described above. Protein concentrations were calculated using the Pierce BCA Protein Assay Kit (LifeTechnologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (20 pg / uL) concentration.UQ / RQ Isolation from worms: Wild type C. elegans (N2) were cultured on Normal Grown media seeded with E. coli OP50-A at 20°C according to Brenner, 1974Animals were washed from plates with S-basal then allowed to settle additional three times to remove bacteria. Pellets were snap frozen in liquid nitrogen and stored at -80 °C until UQ and RQ isolation. To isolate UQ and RQ, 500 pL of 100% LCMS-grade ethanol was added to each tube and then sonicated for 10 seconds, vortexed for 10 seconds, and rested on ice. This process was repeated 10 times to ensure proper solubilization. Samples then had 1 mL of 100% HPLC-grade hexane added and vortexed for 10 minutes in a cold room. Samples were then centrifuged for 10 minutes at 21,300 x g at 4°C. The top (hexane) layer of the sample (containing UQ and RQ) was transferred to a new labeled 1.5 mL Eppendorf tube and dried in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap (Labconco). Samples were stored in -80°C freezer prior to resuspension and running on LC-MS. The bottom layer was discarded and the pellet was saved for protein quantification. Protein concentrations for each sample were calculated using the Pierce BCA Protein Assay Kit (Life Technologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (20 pg / uL) concentration.RQio Standard Preparation: Rhodospirillum rubrum (ATCC 11170, Manassas, VA) was grown anaerobically in four 1-L glass media bottles filled to capacity using yeast extract-supplemented malate-ammonium rich (SMN) medium supplemented with nalidixic acid (20 pg / mL) The 1-L cultures were inoculated from an anaerobic starter culture (16 mL, OD660 of 4.5) and grown at 30 °C for 24 h in the dark, followed by 7 days under direct tungsten illumination (three 40-W bulbs) to a final ODeeo of 2.3. Cells were harvested by centrifugation at 4,000 x g for 15 min at 4 °C and frozen at -80 °C prior to extraction (23 g total pellet mass). A lipid extraction was performed on thawed cells divided equally between twelve 50-mL glass screw-capped centrifuge tubes. Cells (~2 g) in each tube were resuspended in methanol (12 mL) and extracted twice with petroleum ether (2 x 15 mL). Before each separation, the biphasic mixtures were blended at full power using vortex mixing (Vortex Genie 2, Fisher Scientific, Hampton, NH) for 2 min with regular venting and the layers were partitioned using centrifugation (1,000 x g, 4 °C, 5 min). Combined ether extracts were concentrated in vacuo using rotary evaporation.Lipid extracts were purified using three flash column chromatography steps. The crude extract was resuspended in 2 mL of mobile phase (90:10 hexanes / ethyl acetate) and loaded onto a column (3.5 x 20 cm) containing a normal -phase silica gel slurry (Millipore 35-70 pm, Sigma- Aldrich, Burlington, MA) in the same mobile phase. The column was eluted using a gentle air flow with approximately 200 mL mobile phase. Pink-colored fractions containing primarily RQw and RQ9 (10:1 by LC-MS peak areas) with minor amounts of UQ10, UQ9 and RQ« were pooled and concentrated in vacuo. The dried extract was then resuspended in 0.5 mL acetone and loaded onto a column (2 x 13 cm) containing a preparative C-18 slurry (125 A, 55-105 pm, Waters, Milford, MA) in 9: 1 acetone / water. The column was eluted with 400 mL of 9:1 acetone / water and pink-colored fractions were again pooled which contained primarily RQ10 with minor amounts of UQ10 (20:1 by LC-MS peak areas). The combined fractions were concentrated in vacuo to remove acetone. The remaining aqueous slurry containing the quinones (-10 mL) was extracted with hexanes (5 x 5 mL) which created an emulsion that was clarified with ethanol (1 mL) and 2 drops of 6 M KOH. The combined hexane layers were concentrated in vacuo, resuspended in 0.5 mL of 95:5 hexanes / ethyl acetate and applied to a second normal -phase silica column (2 x 13 cm) and eluted using 75 mL of 95:5 hexanes / ethyl acetate to yield >99% pure RQw (654 nmol total, quantified using A283 and RQw molar extinction coefficient, s = 10,994 M-1cm-1in ethanol).RQ9 Standard Preparation: Frozen male Ascaris suum worms (63 g) obtained as a gift from Dr. Catherine Clarke (Department of Chemistry and Biochemistry, UCLA, 2008) were thawed, washed with water and then pulverized for 10 min in a blender (chop and blend settings, Oster 14 speed / 6 cup, Wickliffe, Ohio) using 20 mL petroleum ether. The worm slurry was divided equally between eight 50-mL glass screw-capped centrifuge tubes each containing 3 g glass beads (0.1 mm diameter, BioSpec Products, Bartlesville, OK), and a total of 17 mL methanol, 0.66 mL water and 14 mL petroleum ether were added. The mixtures were further blended using vortex mixing (Vortex Genie 2, Fisher Scientific, Hampton, NH) for 2 min with regular venting and the layers were partitioned using centrifugation (1,000 x g, 4 °C, 5 min) and separated. A second extraction with petroleum ether was performed (12 mL) and the combined ether extracts were dried down using argon gas (Organomation, Berlin, MA).Lipid extracts were resuspended in 0.5 mL hexanes and loaded onto a normal-phase silica column (2 x 20 cm, Millipore 35-70 pm, Sigma- Aldrich, Burlington, MA) that was packed using a 95:5 hexanes / ethyl acetate mobile phase. Using a gentle flow of air, fractions were eluted with 100 mL of the mobile phase followed by 50 mL of 90: 10 hexanes / ethyl acetate. Pink-colored fractions were pooled and concentrated which contained >100:1 RQ9 to RQs by LC-MS peak areas and no UQ. A total of 419 nmol RQ9 (>99% pure) was isolated and quantified using A283 and molar extinction coefficient, e = 10,262 M 'cm1in ethanol.RQ-9 standard curve: Absorbance of the RQ standard diluted in EtOH was measured at 283nm and the concentration of the standard was calculated by the Lambert Beer equation. A calibration curve was obtained by running a dilution series of the standard on LC-MS and measuring the intensity of the RQ peak using TraceFinder 5. 1 (ThermoFisher). Peaks were integrated using a strict 5 ppm mass tolerance. The concentration of RQ in the samples was then calculated with the given equation generated by the RQ linear regression. Ubiquinol and rhodoquinol standards are generated by incubating the oxidized standards with a final concentration of 10 pM NaBFL at room temperature for 15 minutes and analyzing on the LC-MS.MitoSox LC-MS Method: A Q- Exactive orbitrap mass spectrometer with an Ion Max source and HESI II probe attached to a Vanquish Horizon UHLPC system was used to measure all MitoSox reactions. The LC-MS underwent weekly cleaning and calibration with positive and negative Pierce ESI Ion Calibration Calmix (Thermo Scientific). 2 pL of sample was injected into a Supelco Ascentis Express C18 2.7 pm 15 cm x 2.1 mm (Sigma). 2-OH Mitoethidium and Mitosox were measured with modifications to an established protocol. The column oven was set to 25 °C and autosampler was set to 4°C. Buffer A was comprised of water containing 0.1% formic acid while Buffer B was compromised of acetonitrile containing 0.1% formic acid. The liquid chromatography settings were set to an initial flow of 0.25 mL / min at 20% Buffer B. Buffer B increased from 20% to 95% over the span of the first 12 minutes and then dropped down back to 20% within the next minute and was held at that percentage for the last 2 minutes. The mass spectrometry scans were done in full scan (300-700 m / z), positive mode with the spray voltage set to 3.0 kV, heated capillary to 275 °C, HESI probe at 30°C. The sheath gas flow was set at 40 units, auxiliarygas at 15 units, and sweep gas flow at 1 units. The resolution of scan was set to 70,000, AGC target to lxl0A6, and maximum injection time at 100 msec.HKJS-001 & HKJS-003 LC-MS Method: 2 pL of samples were injected onto a Luna 3 pm PFP(2) 100 A, LC Column 100 x 2 mm (Phenomenex). The column oven was held at 25°C and the autosampler tray was held at 4°C. Buffer A contained water with 0.1% formic acid and Buffer B contained acetonitrile with 0.1% formic acid. The gradient was as follows: 0 to 3 min, hold at 30% A, 3 to 3.25 min, gradient to 2% Buffer A, 3.25 to 5 min, hold at 2% Buffer A, 5 to 6 min, gradient to 1% Buffer A, 6 to 8.75 min, hold at 1% Buffer A, 8.75 to 9 min, gradient to 30% Buffer A and 9 to 10 min, hold 30% Buffer A. The chromatographic gradient was run at a flow rate of 0.50 mL / min. The mass spectrometer was operated in full scan, positive-ion mode, with the spray voltage set to 3.0 kV, the heated capillary at 275°C, and the HESI probe at 350°C. The sheath gas flow was 40 units, the auxiliary gas flow was 15 units, and the sweep gas flow was 1 unit. MS data was collected in a range of m / z = 200 -1000. The resolution set at 17,500, the AGC target at 3x106, and the maximum injection time at 250 msec.Polar LC-MS Method: A Q-Exactive orbitrap mass spectrometer with an Ion Max source and HESI II probe attached to a Vanquish Horizon UHLPC system was used to measure polar metabolites. The LC-MS underwent weekly cleaning and calibration with positive and negative Pierce ESI Ion Calibration Calmix (Thermo Scientific). 2 pL of sample was injected into the machine and ran through a SeQuant ZIC-pHILIC 5um 150 x 2.1 mm analytical column (Sigma) with a 2.1 x 20 mm guard column (Sigma) attached to the front end. The column oven was set to 25°C and autosampler was set to 4°C. Buffer A was comprised of 20 mM ammonium carbonate (Sigma), 0.1% ammonium hydroxide (Sigma) in HPLC-grade water (Sigma) and Buffer B was compromised of 100% acetonitrile (Sigma). The liquid chromatography was set to a flow rate of 0. 15 mL / min. First a linear gradient from 80% Buffer B to 20% Buffer B occurred over the course of 20 minutes followed by linear gradient from 20% Buffer B to 80% Buffer B for 0.5 minutes, followed by a hold at 80% Buffer B for 7.5min. The mass spectrometer was set to full scan (70-1000 m / z), polarity switching mode, with the spray voltage set to 4.0 kV, heated capillary to 350°C, and the HESI probe at 30 °C. The sheath gas flow was set at 10 units, auxiliary gas at 1 units, and sweep gas flow at 1 unit. The resolution of scan was set to 70,000, AGC target to IxlO6, and maximum injection time at 20 msec. An additional scan between 220-700 m / z was used to enhance nucleotide detection in the negative mode as well with the maximum injection time set to 80 msec.UQ / RQ LC-MS Method: A Q-Exactive orbitrap mass spectrometer with an Ion Max source and HESI II probe attached to a Vanquish Horizon UHLPC system was used to measure UQ and RQ. The LC-MS underwent weekly cleaning and calibration with positive and negative Pierce ESI Ion Calibration Calmix (Thermo Scientific). 2 pL of sample was injected into the machine and run on a Luna 3 pm PFP(2) 100 A, 100 x 2 mm analytical column (Phenomenex). UQ and RQ were measured with modifications to an established protocol. The column oven was set to 25 °C and autosampler was set to 4°C. Buffer A was comprised of water containing 0.1% formic acid while Buffer B was comprised of acetonitrile containing 0.1% formic acid. The liquid chromatography settings were set at a flow rate of 0.5 mL / min with 70% Buffer B for 3 minutes, then increased to 98% Buffer over 0.25 minutes and held at 98% Buffer B for 1.75 minutes. Buffer B was then increased to 99% over the span of 1 minute and held at 99% Buffer B for 2.75 minutes. Buffer B was then dropped back down to 70% over the span of 1.75 minutes and held at 70% for the two minutes. The mass spectrometry scans were done in full scan (600-1000 m / z), positive mode with the spray voltage set to 4.0 kV, heated capillary to 320 °C, HESI probe at 30 °C, sheath gas flow at 40 units, auxiliary gas at 15 units, and sweep gas flow at 1 unit. The resolution of scan was set to 17,500, AGC target to 3xl0A6, and maximum injection time at 250 msec.For increased sensitivity, a t-SIM (targeted-selected ion monitoring) scan was added to this method, run in positive mode with resolution set at 70,000, AGC target at 1 xlOA6, maximum IT at 250 ms, and an isolation window of 1.0 m / z. The inclusion list comprised of the neutral, proton, and sodium adducts for rhodoquinone-9, rhodoquinol-9, ubiquinone-9, and ubiquinol-9. Rhodoquinol-9 eluted at a retention time of 4.6 minutes, rhodoquinone-9 eluted at 5.3 minutes, ubiquinol-9 eluted at 5.1 minutes, and ubiquinone-9 eluted at 5.7minutes. A table of mass for each molecule with neutral, proton, and sodium adduct is below.For metabolite identity confirmation, a PRM (product reaction monitoring) scan was added to the method, run in positive mode with resolution set at 17,500, AGC target at 2 xl0A5, maximum IT at 150 ms, an isolation window of 0.5 m / z, and (N)CEZstepped nee at 30. The inclusion list for the PRM included rhodoquinone-9, rhodoquinol-9, ubiquinone-9, ubiquinol-9 masses for proton adducts. RQ-9 and RQH2-9 were monitored throughout the 4-6-minute window while UQ-9 and UQH2-9 were monitored throughout the 5-7-minute window. MS2 fragmentation of RQ-9 and RQH2-9 metabolites was utilized to confirm its identity.LC-MS Data Analysis. Metabolomics data were analyzed using TraceFinder 5.1 (ThermoFisher). Peaks were integrated using a strict 5 ppm mass tolerance and attention to the retention times as determined by purified standards of the respective metabolites.13C and15N-isotopologues were integrated with the same retention time as the12C and14N- isotopologues. All stable isotope tracing data underwent natural abundance correction using IsoCorrectoR (Bioconductor).Quantification and Statistical Analysis. The statistical tests used for each experiment are listed in the figure legends. 0.05 was the alpha used as the significance threshold. Statistical significance was usually calculated in GraphPad Prism. N represents the number of biological replicates (seeded cells or mice) in a given experiment.Synthesis of Rhodoquinone Mimetics HKJS-001 and HKJS-003 Synthetic scheme for the preparation of 2-amino-5-decyl-3-methoxy-6- methylcyclohexa-2,5-diene-l, 4-dione (HKJS-001)Step-1: Synthesis of 2,3,4-trimethoxy-6-methylbenzaldehyde (2)Procedure: To a stirred solution of l,2,3-trimethoxy-5-methylbenzene (1) (25 g, 137.4 mmol, 1.0 eq.) in DMF (15 g, 206.1 mmol, 1.5 eq.) at 0 °C was added POCh (31.5 g, 206.1 mmol, 1.5 eq.). The resultant reaction mixture was stirred at room temperature for 24 h, then 45 °C for 1 h. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and extracted with ethyl acetate (2 X 100 mL). The organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford 2,3,4-trimethoxy-6-methylbenzaldehyde (2) (22 g, Yield: 76.3 %) as an off white solid;‘HNMR (400 MHz, CDCh): 5 10.04 (s, 1H), 6.51 (s, 1H), 3.99 (s, 3H), 3.92 (s, 3H), 3.86 (s, 3H), 2.57 (s, 3H)Step-2: Synthesis of 2-hydroxy-3,4-dimethoxy-6-methylbenzaIdehyde (3)Procedure: To a stirred solution of 2, 3, 4-trimethoxy-6- methylbenzaldehyde (2) (24 g, 114.2 mmol, 1.0 eq.) in DCM (240 mL, 10 vol.) at -78 °C was added BBri (97.1 mL, 97.1 mmol, 0.85 eq.). The resultant reaction mixture was stirred at room temperature for 2 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and extracted with DCM (2 X 150 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-30% gradient elution of EtOAc in Pet-ether afforded 2-hydroxy-3,4-dimethoxy-6-methylbenzaldehyde (3) (16.3 g, Yield 73 %) as an off white solid.‘HNMR (400 MHz, CDCh): 5 12.20 (s, 1H), 10.13 (s, 1H), 6.32 (s, 1H), 3.93 (s, 3H), 3.86 (s, 3H), 2.56(s, 3H).Step-3: Synthesis of 2-(benzyloxy)-3,4-dimethoxy-6-methylbenzaIdehyde (4)Procedure: To a stirred solution of 2 -hydroxy-3 ,4-dimethoxy-6- methylbenzaldehyde (3) (18.7 g, 95.66 mmol, 1.0 eq.) in DMF (187 mL, 10 vol) at 0 °C was added K2CO3 (39.6 g, 286.9 mmol, 3 eq.) and benzyl bromide (17.0 mL, 143.4 mmol, 1.5 eq.). The resultant reaction mixture was stirred at 60 °C for 3 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and stirred for 20 min. The precipitated compound was filtered and washed with hexane (50 mL) to afford 2-(benzyloxy)-3,4-dimethoxy-6-methylbenzaldehyde (4) (25 g, Yield: 92 %) as an off white solid;’HNMR (400 MHz, CDCh): 5 10.35 (s, 1H), 7.44-7.34 (m, 5H), 6.53 (s, 1H), 5.17 (s, 2H), 3.94 (s, 3H), 3.89 (s, 3H), 2.55 (s, 3H).Step-4 & 5: Synthesis of 2-(benzyloxy)-3,4-dimethoxy-6-methylphenol (5)Procedure: To a stirred solution of 2-(benzyloxy)-3,4-dimethoxy-6- methylbenzaldehyde (4) (25 g, 87.32 mmol, 1.0 eq.) in ethyl acetate (250 mL, 10 vol.) at room temperature was added m-CPBA (18.7 g, 104.7 mmol, 1.2 eq.) The resultant reaction mixture was stirred at room temperature for 24 h. After completion of the reaction as indicated by TLC, KF (30 g, 517.2 mmol, 6 eq.) was added to the reaction mixture and stirred for 1 h. The reaction mixture was filtered and the filtrate was concentrated under reduced pressure. The residue was diluted with 1 ,4-dioxane (50 mL) and added 3N KOH solution (60 mL) slowly, and stirred at room temperature for 1 h. The reaction mixture was diluted with ice water (100 mL), and extracted with EtOAc (2 X 100 mL), the organic layer was dried over sodium sulphate, concentrated under reduced pressure afforded (28 g, crude) and purified by silica gel column chromatography (100-200 mesh) with 0-30% gradient elution of EtOAc in pet-ether afforded 2-(benzyloxy)-3,4-dimethoxy-6-methylphenol (5) (20 g, Yield: 83 %) as an off white solid.’HNMR (400 MHz, CDCh): 5 7.44-7.29 (m, 5H), 6.45 (s, 1H), 5.40 (s, 1H), 5.11 (s, 2 H), 3.90 (s, 3H), 3.82 (s, 3H), 2.18 (s, 3H).Step-6: Synthesis of 3-(benzyloxy)-2-methoxy-5-methylcyclohexa-2,5-diene-l,4- dione (6)Procedure: To a stirred solution of 2-(benzyloxy)-3,4-dimethoxy-6-methylphenol(5) (10 g, 36.5 mmol, 1.0 eq.) in acetonitrile: water (100 mL, 7:3, 10 vol.), was added 2,6pyridine dicarboxylic acid (15.2 g, 91.2 mmol, 2.5 eq.) at 0 °C. To the reaction mixture, ceric ammonium nitrate (50 g, dissolved in 50 mL 1 :1 mixture of acetonitrile water) was added drop wise over a period of 15 min. The resultant reaction mixture was stirred at 0 °C for 1 h and at room temperature for 1 h. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and extracted with DCM (2 X 100 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford the crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-20% gradient elution of EtOAc in pet-ether to afford 3-(benzyloxy)-2-methoxy-5-methylcyclohexa-2,5-diene-l, 4-dione (6) (6.7 g, Yield: 71 %) as an orange liquid.'HNMR (400 MHz, CDCh): 5 7.41-7.23 (m, 5H), 6.42 (s, 1H), 5.21 (s, 2H), 3.95 (s, 3H), 2.04 (s, 3H).Step-7: Synthesis of 2-(benzyloxy)-5-decyl-3-methoxy-6-methylcyclohexa-2,5- diene- 1,4-dione (7)Procedure: To a stirred solution of 3-(benzyloxy)-2-methoxy-5-methylcyclohexa- 2, 5 -diene- 1,4-dione (6) (70 mg, 0.27 mmol, 1.0 eq.) and undecanoic acid (6A) (75 mg, 0.4 mmol, 1.5 eq.) in acetonitrile (1.5 mL, 22 vol.). To the reaction mixture, was added AgNOr (18.7 mg, 0.11 mmol, 1.5 eq.). The reaction mixture was heated to 80 °C. To the heated reaction mixture was added K2S2O8 (146 mg dissolved in water 1.5 mL, 0.54 mmol, 2 eq.) drop wise over 5 min. After 1 h, completion of the reaction as indicated by TLC. The reaction mixture was diluted with ice water (20 mL), and extracted with DCM (2 X 20 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afforded crude. The crude material was purified by silica gel column chromatography (100-200 mesh) with 0-20% gradient elution of EtOAc in pet-ether to afford 2-(benzyloxy)-5-decyl-3-methoxy-6-methylcyclohexa-2,5-diene- 1,4-dione (7) (40 mg, Yield: 37 %) as a low melting orange solid.'HNMR (400 MHz, CDCh): 5 7.44-7.33 (m, 5H), 5.20 (s, 2H), 3.92 (s, 3H), 2.46- 2.42 (m, 2H), 2.02 (s, 3H), 1.33-1.25 (m, 16 H), 0.89-0.89 (m, 3H).Step-8: Synthesis of 2-decyl-5-hydroxy-6-methoxy-3-methylcyclohexa-2,5- diene- 1,4-dione (8)Procedure: To a stirred solution of 2-(benzyloxy)-5-decyl-3-methoxy-6- methylcyclohexa-2,5-diene-l, 4-dione (7) (33 mg, 0.08 mmol, 1.0 eq.) in DCM (0.8 mL) was added SnCh solution (IM in DCM, 0.016 mmol, 0.016 mL, 0.2 eq.) drop wise at -20°C. The resultant reaction mixture was stirred at 0 °C for 3 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (5 mL), and extracted with DCM (2 X 10 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford the crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-20 % gradient elution of EtOAc in pet- ether to afford 2-decyl-5-hydroxy-6-methoxy-3-methylcyclohexa-2,5-diene- 1,4-dione (8) (25 mg, Yield: 98 %) as a dark pink solid.'HNMR (400 MHz, DMSO): 5 10.31 (s, 1H), 3.75 (s, 3H), 2.39-2.36 (m, 2H), 1.92 (s, 3H), 1.35-1.16 (m, 16 H), 0.86-0.83 (m, 3H).Step-9: Synthesis of 4-decyl-2-methoxy-5-methyl-3,6-dioxocyclohexa-l,4-dien-l- yl methane sulfonate (9)Procedure: To a stirred solution of 2-decyl-5-hydroxy-6-methoxy-3- methylcyclohexa-2,5-diene-l ,4-dione (8) (25 mg, 0.081 mmol, 1.0 eq.) in DCM, Et<N (24.6 mg, 0.243 mmol, 3.0 eq.) was added at -20 °C and stirred for 10 min. Mesylchloride (18.6 mg, 0.16 mmol, 2.0 eq.) was added drop wise at -20 °C. The resultant reaction mixture was stirred at room temperature for 16 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with diluted with ice water (10 mL), and extracted with ethyl acetate (2 X 10 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford 4-decyl-2-methoxy-5- methyl-3,6-dioxocyclohexa-l,4- dien-l-yl methane sulfonate (9) (30 mg, crude). The crude material was used as such without further purification.Step- 10: Synthesis of 2-azido-5-decyI-3-methoxy-6-methylcydohexa-2,5-diene- 1, 4-dione (10)Procedure: To a stirred solution of 4-decyl-2-methoxy-5-methyl-3,6- dioxocyclohexa-l,4-dien-l-yl methanesulfonate (9) (500 mg, 1.25 mmol, 1.0 eq.) in MeOH (10 vol.), NaNa (164 mg, 2.52 mmol, 2.02 eq.) was added at room temperature. The resultant reaction mixture was stirred at room temperature for 16 h. After completion of reaction as indicated by TLC, reaction mixture was diluted with diluted with ice water (20 mL), and extracted with ethyl acetate (2 X 20 mL), organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afforded the crude. Crude was purified by silica gel column chromatography (100-200 mesh) with 0-10 % gradient elution of EtOAc in pet-ether to afford 2-azido-5-decyl-3-methoxy-6-methylcyclohexa-2,5-diene- 1, 4-dione (10) (230 mg, Yield: 55 %) as a yellow liquid.‘HNMR (400 MHz, CDCh): 5 4.07 (s, 3H), 2.48-2.44 (m, 2H), 2.04 (s, 3H), 1.33- 1.26 (m, 16 H), 0.90-0.86 (m, 3H).Step-11: Synthesis of 2-amino-5-decyl-3-methoxy-6-methylcyclohexa-2,5-diene-1.4-dione (HKJS-001)Procedure: To a stirred solution of 2-azido-5 -decyl-3 -methoxy-6-methylcyclohexa-2.5 -diene- 1,4-dione (10) (300 mg, 0.90 mmol, 1.0 eq.) in THF (15 mL, 50 vol.), TPP (235 mg, 0.90 mmol, 1.0 eq.) was added. The reaction mixture was stirred for 2 h at room temperature. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with diluted with ice water (50 mL), and extracted with ethyl acetate (2 X 50 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford the crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-10 % gradient elution of EtOAc in pet-ether afforded semi-pure compound, which was purified by preparative HPLC [column: Gemini Cl 8 (21.2*250mm)5p, mobile phase A: 10 mm AB in water, mobile phase B: 100% ACN; program (time% B): 0 / 50, 3 / 50, 10 / 90, 15 / 95, flow rate: 14 mL / min]. The collected pure fractions were combined and lyophilized to afford 2-amino-5-decyl-3-methoxy-6- methylcyclohexa-2,5-diene-l, 4-dione (HKJS-0001) (36 mg, Yield: 13 %)LC-MS (ESI) m / z: 308 [M+H]+; HPLC: 99.6%'H-NMR (400 MHz, DMSO-rf6): 5 6.31 (brs, 2H), 3.62 (s, 3H), 2.39-2.35 (m, 2H), 1.88 (s, 3 H), 1.28-1.24 (m, 16H), 0.86-0.83 (t, J = 6.8 Hz, 3H).13C-NMR (100 MHz, DMSO-d6): 5 185.6, 179.9, 144.5, 138.5, 135.1, 133.3, 59.7, 31.7, 29.6, 29.4, 29.3, 29.2, 29.1, 28.9, 26.2, 22.6, 14.4, 11.8.Synthetic scheme for the preparation of (10-(4-amino-5-methoxy-2-methyl-3,6- dioxocyclohexa-l,4-dien-l-yl)decyl)triphenylphosphonium (HKJS-003)Step-1: Synthesis of 2,3,4-trimethoxy-6-methylbenzaldehyde (2)Procedure: To a stirred solution of l,2,3-trimethoxy-5-methylbenzene (1) (25 g, 137.4 mmol, 1.0 eq.) in DMF (15 g, 206.1 mmol, 1.5 eq.) at 0 °C was added POCh (31.5 g, 206.1 mmol, 1.5 eq.). The resultant reaction mixture was stirred at room temperature for 24 h, then 45 °C for 1 h. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and extracted with ethyl acetate (2 X 100 mL). The organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford 2,3,4-trimethoxy-6-methylbenzaldehyde (2) (22 g, Yield: 76.3 %) as an off white solid;'HNMR (400 MHz, CDCh): 5 10.04 (s, 1H), 6.51 (s, 1H), 3.99 (s, 3H), 3.92 (s, 3H), 3.86 (s, 3H), 2.57 (s, 3H).Step-2: Synthesis of 2-hydroxy-3,4-dimethoxy-6-methylbenzaldehyde (3)Procedure: To a stirred solution of 2,3,4-trimethoxy-6-methylbenzaldehyde (2) (24 g, 114.2 mmol, 1.0 eq.) in DCM (240 mL, 10 vol.) at -78 °C was added BB (97.1 mL, 97.1 mmol, 0.85 eq.). The resultant reaction mixture was stirred at room temperature for 2 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and extracted with DCM (2 X 150 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-30% gradient elution of EtOAc in Pet-ether afforded 2-hydroxy-3,4-dimethoxy-6-methylbenzaldehyde (3) (16.3 g, Yield 73 %) as an off white solid.‘HNMR (400 MHz, CDCh): 5 12.20 (s, 1H), 10.13 (s, 1H), 6.32 (s, 1H), 3.93 (s, 3H), 3.86 (s, 3H), 2.56(s, 3H).Step-3: Synthesis of 2-(benzyloxy)-3,4-dimethoxy-6-methylbenzaIdehyde (4)Procedure: To a stirred solution of 2 -hydroxy-3 ,4-dimethoxy-6- methylbenzaldehyde (3) (18.7 g, 95.66 mmol, 1.0 eq.) in DMF (187 mL, 10 vol) at 0 °C was added K2CO3 (39.6 g, 286.9 mmol, 3 eq.) and benzyl bromide (17.0 mL, 143.4 mmol, 1.5 eq.), The resultant reaction mixture was stirred at 60 °C for 3 h. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL), and stirred for 20 min. The precipitated compound was filtered and washed with hexane (50 mL) to afford 2-(benzyloxy)-3,4-dimethoxy-6-methylbenzaldehyde (4) (25 g, Yield: 92 %) as an off white solid;’HNMR (400 MHz, CDCh): 5 10.35 (s, 1H), 7.44-7.34 (m, 5H), 6.53 (s, 1H), 5.17 (s, 2H), 3.94 (s, 3H), 3.89 (s, 3H), 2.55 (s, 3H).Step-4 & 5: Synthesis of 2-(benzyloxy)-3,4-dimethoxy-6-methylphenol (5)Procedure: To a stirred solution of 2-(benzyloxy)-3,4-dimethoxy-6- methylbenzaldehyde (4) (25 g, 87.32 mmol, 1.0 eq.) in ethyl acetate (250 mL, 10 vol.) at room temperature was added m-CPBA (18.7 g, 104.7 mmol, 1.2 eq.) The resultant reaction mixture was stirred at room temperature for 24 h. After completion of the reaction as indicated by TLC, KF (30 g, 517.2 mmol, 6 eq.) was added to the reaction mixture and stirred for 1 h. Reaction mixture was filtered, and the fdtrate was concentrated under reduced pressure. The residue was diluted with 1 ,4-dioxane (50 mL) and added 3N KOH solution (60 mL) slowly and stirred at room temperature for 1 h. The reaction mixture was diluted with ice water (100 mL), and extracted with EtOAc (2 X 100 mL), the organic layer was dried over sodium sulphate, concentrated under reduced pressure afforded (28 g, crude) and purified by silica gel column chromatography (100-200 mesh) with 0-30% gradient elution of EtOAc in pet-ether afforded 2-(benzyloxy)-3,4-dimethoxy-6-methylphenol (5) (20 g, Yield: 83 %) as an off white solid’HNMR (400 MHz, CDCh): 5 7.44-7.29 (m, 5H), 6.45 (s, 1H), 5.40 (s, 1H), 5.11 (s, 2 H), 3.90 (s, 3H), 3.82 (s, 3H), 2.18 (s, 3H).Step-6: Synthesis of 3-(benzyloxy)-2-methoxy-5-methylcyclohexa-2,5-diene-l,4- dione (6)Procedure: To a stirred solution of 2-(benzyloxy)-3,4-dimethoxy-6-methylphenol(5) (10 g, 36.5 mmol, 1.0 eq.) in acetonitrile: water (100 mL, 7:3, 10 vol.), was added 2,6pyridine dicarboxylic acid (15.2 g, 91.2 mmol, 2.5 eq.) at 0 °C. To the reaction mixture, ceric ammonium nitrate (50 g, dissolved in 50 mL 1 :1 mixture of acetonitrile water) was added drop wise over a period of 15 min. The resultant reaction mixture was stirred at 0 °C for 1 h and at room temperature for 1 h. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with ice water (100 mL) and extracted with DCM (2 X 100 mL), the organic layer was dried over sodium sulphate, concentrated under reduced pressure to afford the crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-20% gradient elution of EtOAc in pet-ether afforded 3-(benzyloxy)- 2-methoxy-5-methylcyclohexa-2, 5-diene-l, 4-dione (6) (6.7 g, Yield: 71 %)‘HNMR (400 MHz, CDCh): 5 7.41-7.23 (m, 5H), 6.42 (s, 1H), 5.21 (s, 2H), 3.95 (s, 3H), 2.04 (s, 3H)Step-7: Synthesis of 2-(benzyloxy)-5-(10-bromodecyI)-3-methoxy-6- methylcycIohexa-2,5-diene- 1 ,4-dione (7)Procedure: To a stirred solution of 3-(benzyloxy)-2-methoxy-5-methylcyclohexa- 2, 5-diene-l, 4-dione (6) (2 g, 7.75 mmol, 1.0 eq.) and 11 -bromoundecanoic acid (6A) (3.0 g, 11.62 mmol, 1.5 eq.) in acetonitrile (44 mL, 22 vol.). To the reaction mixture, was added AgNCL (526 mg, 3.11 mmol, 0.4 eq.). The reaction mixture was heated to 80 °C and added K2S2O8 (4.18 g dissolved in water 44 mL, 15.5 mmol, 2 eq.) drop wise at 80 °C over a period of 30 min. After 1 hour, completion of the reaction was indicated by TLC. The reaction mixture was diluted with ice water (20 mL), and extracted with DCM (2 X 20 mL), the organic layer was dried over sodium sulphate, concentrated under reduced pressure to afford the crude. The crude material was purified by silica gel column chromatography (100-200 mesh) with 0-10% gradient elution of EtOAc in pet-ether to afford 2-(benzyloxy)- 5-(10-bromodecyl)-3-methoxy-6-methylcyclohexa-2, 5-diene-l, 4-dione (7) (320 mg, Yield: 8.7 %) as an orange liquid.'HNMR (400 MHz, CDCh): 5 7.44-7.42 (m, 1H), 7.39-7.34 (m, 4H), 5.20 (s, 2H), 3.92 (s, 3H), 3.47 (t, J = 6.8 Hz, 2H), 2.46-2.42 (m, 2H), 2.07 (s, 3H), 1.87-1.83 (m, 4H), 1.41-1.26 (m, 12 H)Step-8: Synthesis of 2-(10-bromodecyl)-5-hydroxy-6-methoxy-3- methy!cyclohexa-2,5-diene- 1,4-dione (8)Procedure: To a stirred solution of 2-(benzyloxy)-5-(10-bromodecyl)-3-methoxy-6- methylcyclohexa-2, 5-diene-l, 4-dione (7) (1.2 g, 2.52 mmol, 1.0 eq.) in DCM (24 vol.), was added IM SnCL solution (1 mL, 1.01 mmol, 0.4 eq.) drop wise at -20 °C. The resultantreaction mixture was stirred at 0 °C for 3 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (50 mL), and extracted with DCM (2 X 30 mL), the organic layer was dried over sodium sulphate, concentrated under reduced pressure to afford the crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-20 % gradient elution of EtOAc in pet-ether to afford 2-(10- bromodecyl)-5-hydroxy-6-methoxy-3-methylcyclohexa-2,5-diene-l, 4-dione (8) (780 mg, Yield: 80 %) as a dark pink solid.'HNMR (400 MHz, CDCh): 5 6.51 (brs, 1H), 4.07 (s, 3H), 3.41 (t, J = 7.2 Hz, 2H) 2.46 (t, 7 = 7.2 Hz, 2H), 2.04 (s, 3H), 1.88-1.81(m, 2 H), 1.65-1.60 (m, 2 H), 1.43-1.28 (m, 12H).Step-9: Synthesis of 4-(10-bromodecyl)-2-methoxy-5-methyl-3,6- dioxocyclohexa-l,4-dien-l-yl methanesulfonate (9)Procedure: To a stirred solution of 2-(10-bromodecyl)-5-hydroxy-6-methoxy-3- methylcyclohexa-2,5-diene-l, 4-dione (8) (780 mg, 2.02 mmol, 1.0 eq.) in DCM, EhN (613 mg, 6.06 mmol, 3 eq.) was added at -20 °C and stirred for 10 min. Mesyl chloride was added (462 mg, 4.04 mmol, 2.0 eq.) drop wise at -20°C. The resultant reaction mixture was stirred at room temperature for 16 h. After completion of the reaction as indicated by TLC, the reaction mixture was diluted with ice water (25 mL), and extracted with ethyl acetate (2 X 20 mL), the organic layer was dried over sodium sulphate, concentrated under reduced pressure to afford crude material. The crude material was purified by silica gel column chromatography (100- 200 mesh) using 0 to 10% EtOAc in pet ether as an eluent to afford 4-(10-bromodecyl)-2-methoxy-5-methyl-3,6-dioxocyclohexa-l,4-dien-l-yI methanesulfonate (9) (500 mg, Yield 53%) as a yellow liquid.'HNMR (400 MHz, CDCh): 5 4.23 (s, 3H), 3.52 (s, 3H), 3.40 (t, J = 6.8 Hz, 2 H), 2.46 (t, J = 6.8 Hz, 2H), 2.05 (s, 3H), 1.89-1.82 (m, 2H), 1.43-1.33 (m, 14 H).Step- 10: 2-azido-5-(10-bromodecyl)-3-methoxy-6-methylcyclohexa-2,5-diene- 1, 4-dione (10)Procedure: To a stirred solution of 4-(10-bromodecyl)-2-methoxy-5-methyl-3,6- dioxocyclohexa-l,4-dien-l-yl methanesulfonate (9) (25 mg, 0.053 mmol, 1.0 eq.) in MeOH (0.5 mL, 18 vol.) was added NaNs (7 mg, 0.10 mmol, 2.02 eq.) at 0°C. The resultant reaction mixture was stirred at room temperature for 16 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (10 mL), and extracted with ethyl acetate (2 X 10 mL), the organic layer was dried over sodium sulphate,concentrated under reduced pressure to afforded the crude. The crude compound was purified by silica gel column chromatography (100-200 mesh) with 0-10 % gradient elution of EtOAc in pet-ether afforded 2-azido-5-(10-bromodecyl)-3-methoxy-6- methylcyclohexa-2,5-diene-l, 4-dione (10) (16 mg, Yield: 75 %) as an orange liquid'HNMR (400 MHz, CDCh): 5 4.07 (s, 3H), 3.40 (t, J= 6.8 Hz, 2H), 2.46 (t, J= 6.8 Hz, 2H), 2.04 (s, 3H), 1.89-1.81 (m, 2H), 1.43-1.25 (m, 14 H).Step-11: Synthesis of 2-amino-5-(10-bromodecyl)-3-methoxy-6- methylcyclohexa-2,5-diene- 1,4-dione (11)Procedure: To a stirred solution of 2-azido-5-(10-bromodecyl)-3-methoxy-6- methylcyclohexa-2,5-diene-l, 4-dione (10) (280 mg, 0.68 mmol, 1.0 eq.) in THF (28 mL, 100 vol.), TPP (267 mg, 1.02 mmol, 1.5 eq.) was added. The reaction mixture was stirred at room temperature for 2 h. After completion of reaction as indicated by TLC, the reaction mixture was diluted with ice water (10 mL), and extracted with ethyl acetate (2 X 10 mL), the organic layer was dried over anhyd. sodium sulphate, concentrated under reduced pressure to afford the crude. The crude was purified by silica gel column chromatography (100-200 mesh) with 0-20 % gradient elution of EtOAc in pet-ether 2-amino-5-(10- bromodecyl)-3-methoxy-6-methylcydohexa-2,5-diene-l, 4-dione (11) (230 mg, Yield: 81 %) as red color solid.LC-MS (ESI) m / z:386 [M+H]+'HNMR (400 MHz, CDCh): 5 4.68 (brs, 2H), 3.87 (s, 3H), 3.41 (t, J = 6.8 Hz, 2H), 2.45 (t, J = 6.8 Hz, 2H), 1.97 (s, 3H), 1.87-1.81 (m, 2H), 1.40-1.25 (m, 14H).Step- 12: Synthesis of (10-(4-amino-5-methoxy-2-methyl-3,6-dioxocycIohexa-l,4- dien- 1 -yl)decyl)triphenylphosphonium (HK J S -003)To a stirred solution of 2-amino-5-(10-bromodecyl)-3-methoxy-6-methylcyclohexa- 2, 5 -diene- 1,4-dione (11) (285 mg, 0.738 mmol, 1.0 eq.) in DMF (8 mL, 20 vol.), TPP (483 mg, 1.84 mmol, 2.5 eq.) was added. The reaction mixture was stirred at 90 °C for 16 h. After completion of reaction as indicated by TLC, the reaction mixture was concentrated under reduced pressure to get the crude material. The crude material was purified by grace reverse phase column with 0-80 % gradient elution of water / acetonitrile to afford (10-(4- amino-5-methoxy-2-methyI-3,6-dioxocydohexa- 1,4-dien- 1- yl)decyl)triphenylphosphonium (HKJS-003) (31.4 mg, Yield: 6%) as a hygroscopic purple solid.LC-MS (ESI) m / z: 568 [M]+HPLC: 97.5%'HNMR (400 MHz, DMSO-rf6): 57.92-7.87 (m, 3H), 7.82-7.74 (m, 12 H), 6.33 (brs, 2H), 3.61 (s, 3H), 3.59-3.51 (m, 2H), 2.38-2.32(m, 2H), 1.87 (s, 3H), 1.52-1.42 (m, 4H), 1.33-1.25 (m, 12H).13C-NMR (100 MHz, DMSO-rf6): 5 185.6, 179.9, 144.5, 138.6, 135.3, 135.1, 134.1 (d, 7 = 10 Hz, PhC-2), 133.3, 130.7 (d, 7 = 12 Hz, PhC-3), 118.8 (d, 7 = 86 Hz, PhC-1), 59.7, 30.2 (d, 7 = 17 Hz, P-CH2- CH2-), 29.6, 29.5, 29.2, 29.1, 28.9, 28.5, 26.2, 22.2, 20.6 (d, 7 = 50 Hz, P-CH2), 11.8.ResultsRhodoquinone is Present in Mammalian Mitochondria and Varies Across TissuesHypoxia or ETC inhibition diverts electrons onto fumarate through SDH reversal, enabling ETC-dependent pyrimidine synthesis and hydrogen sulfide oxidation. Mechanistically, UQH2accumulation is required to overcome the thermodynamic barrier of fumarate reduction. However, certain tissues, particularly the kidney, liver, and brain, possess a remarkable ability to catalyze fumarate reduction. The pO2of the kidney (15-70 mmHg), liver (30-60 mmHg), and brain (20-40 mmHg), exceeds the binding constant of O2for complex IV (0.6-6 mmHg), suggesting that O2isn’t limiting for electron removal from the ETC. Purified mitochondria from mouse kidney and brain displayed SDH-dependent fumarate reduction, and the rate of fumarate reduction was comparable to that of succinate oxidation, despite this reaction being catalyzed in plentiful atmospheric O2(Figure 1 A). Moreover, UQH2abundance didn’t correlate with the propensity for a tissue to catalyze fumarate reduction (Figure IB, Figures 7A-7C). Thus, an alternative mechanism, other than O2availability or UQH2accumulation, underlies fumarate reduction.Eukaryotes such as snails; mussels; oysters; and nematodes, parasitic helminths, protists, and bacteria, possess the electron carriers menaquinone (MQ) and rhodoquinone (RQ). MQ and RQ have a lower E o than fumarate, allowing electron transfer to fumarate in the ETC. UQ is the only known mammalian electron carrier and has a standard reduction potential of + 100 mV (Figure 1C). Previous attempts to identify alternative electron carriers in mammals have been largely restricted to the heart. Moreover, studies on mammalian tissues have mainly analyzed electron carriers in their oxidized form, limiting detection, especially if the reduced form dominates. Finally, approaches to measure other electroncarriers were often done using HPLC-UV-vis, which is less sensitive than current mass spectrometry technologies.To determine if mammalian mitochondria possess other electron carriers, mitochondria were isolated from mouse tissues, quinones were extracted in a manner that stabilizes the reduced form, and samples were analyzed on liquid-chromatography mass spectrometry (LC-MS). Electron carriers possess a quinone head and a poly-isoprene tail. Quinones with six isoprene units or more are hydrophobic enough to embed in the inner membrane. As expected, UQ with a 9 isoprene unit tail (UQ9), and its reduced form ubiquinol-9, were detected in all tissues (Figure ID, Figures 7D-7J). Peaks that corresponded to the m / z for RQ with a 9 isoprene units (RQ9), and its reduced form rhodoquinol-9, were also detected (Figures ID- IL, Figures 7D-7J, and Figure 8G). The major and minor isoprene tail lengths, respectively, are 9 and 10 for both UQ and RQ (Figure 8G). UQs is also detectable, whereas RQs was below the detection limit or not present (Figure 8G). There were no detectable peaks that corresponded to the mass to charge ratio m / z for MQ and menaquinol up to 10 isoprene units (Figure 8G).The identity and subcellular localization of RQ was confirmed in many ways. RQ9 from C. elegans and mouse tissues matched in retention time and fragmentation patterns (Figure IE, Figures 8H-8Q). Also, RQ9 was purified from the nematode Ascaris siaim, further confirming the retention time and fragmentation patterns in mouse tissues and allowing for absolute quantification (Figure IF, Figures 7K-7L). Fragmentation of rhodoquinol-9 and RQ9 in mouse tissues matched the fragmentation patterns of the standards and C. elegans (Figures 8H-8Q). Finally, when comparing whole tissue versus mitochondrial extracts, RQ9, like UQ9, is enriched in the mitochondrial compartment (Figures 1G-H, 8A-8F). RQ was most abundant in mitochondria from the brain, kidney, and pancreas (Figure IF). The oxidized form, RQ9, was 4500-fold more abundant in kidney than other tissues (Figure 7D). Rhodoquinol-9 was 50-100-fold more abundant in the brain than other tissues (Figure 7E). C. elegans have a RQ:UQ ratio of approximately 1 :2 (Figure II). The RQ:UQ ratio in the brain is approximately 1:3, and the rest of the tissues have much lower RQ:UQ ratios ranging from approximately 1:50 to 1:100 (Figure 7J). As the levels of RQ are much lower than UQ, it is likely that this metabolite isn’t ubiquitously synthesized or is enriched in specific tissue niches.Human cells predominantly synthesize UQ with 10 isoprene units (UQ10). RQ10 was extracted from Rhodospirillum rubrum, purified, and displayed expected chromatographicand fragmentation patterns (Figure 9A). Mitochondria isolated from human brain, kidney, and muscle had RQio (Figures 1I-1K, Figure 9B). The ratios of RQio ■ UQw in human tissues were 1:5, 1:50, and 1:100 in the brain, kidney, and muscle, respectively (Figure II). These ratios are much lower than C. elegans, implying that RQ synthesis in humans is likely cell-type or regional specific. Taken together, these data reveal that RQ is present in mouse and human mitochondria.Rhodoquinone carries electrons to fumarate in the mammalian ETCThe standard reduction potential of RQ (-63 mV) is lower than fumarate (+30 mV), enabling thermodynamically favorable fumarate reduction in C. elegans, parasitic helminths, and bacteria. Although RQ is detected in mouse and human tissues, it is undetectable in a panel of cancer cells cultured in vitro in normoxia and hypoxia (Figure 2B, Figures 9C-9J). Primary hepatocytes isolated from mouse liver displayed a progressive decrease in RQ9, but not UQ9 over time (Figure 9K), suggesting that RQ synthesis is suppressed in vitro. The disparity in RQ synthesis in vitro and in vivo could be attributed to an incomplete biosynthetic pathway in mammalian cells. C. elegans synthesize RQ de novo through the kyneurenine pathway. The isoprene tail is synthesized and attached using similar enzymes as UQ biosynthesis. A splice variant of polyprenyltransferase (CoQ-2), which attaches the isoprene tail to the quinone head, is required for RQ synthesis in C. elegans. Since mammals don’t possess this isoform, their RQ acquisition pathway is likely distinct from that of C. elegans.To facilitate studies of RQ in mammalian cells, we developed a genetic tool that enables RQ synthesis. Rhodospirillum rubrum synthesize RQ directly from UQ using the enzyme RquA, which swaps a methoxy group on the quinone head of UQ with an amine (Figure 2B). Ectopic RquA expression in Escherichia coli and Saccharomyces cerevisiae enables their synthesis of RQ. Using a similar strategy, we engineered RquA with a C- terminal FLAG tag and an N-terminal mitochondrial localization signal and expressed it in 143B osteosarcoma and Caki-1 renal cell carcinoma cells on a doxycycline-inducible promoter. RquA localized to the mitochondrial compartment and didn’t alter mitochondrial content or ETC complex formation as measured by immunoblotting and native gel analysis of ETC complexes in purified mitochondria (Figures 9L-9P). RquA decreased UQ10 and increased RQio, up to an 8:1 RQ to UQ ratio (Figure 2C, Figure 9Q), providing a system to study the role of RQ in mammals with minimal UQ interference.To determine if RQ carries electrons in the mammalian ETC, reduction of both electron acceptors were monitored. RquA expression decreased complex Ill-dependent O2 consumption while the same doxycycline concentrations used to induce RquA had no effect on wild-type cells (Figure 9R). To test if RQ delivers electrons onto fumarate via SDH, wild-type and RquA-expressing cells were subjected to13Cs-glutamine and13C4-aspartate tracing assays (Figures 2D-2E). In the glutamine tracing assay, succinate oxidation is monitored by the incorporation of13Cs-glutamine into13C4-succinate and13C4-fumarate, and their ratio is a proxy for succinate oxidation. Fumarate reduction is monitored by the incorporation of13C5-glutamine into13C3-fumarate and13C3-succinate, and their ratio is a proxy for fumarate reduction. Complex III inhibition by Antimycin caused UQH2 accumulation and SDH reversal, indicative of fumarate reduction (Figure 2F, Figures 10A- 10B). Similarly, RquA expression increased fumarate reduction and decreased succinate oxidation in a panel of cell lines cultured in normoxia, without altering the UQ:UQH2 ratio (Figure 2F, Figures 10A-10C). Thus, RQ itself, as opposed to UQH2 accumulation, drives fumarate reduction independently of O2 availability (Figure 10C).Fumarate is an electrophile that can be non-enzymatically reduced to succinate. Next, the SDH-dependence of RQ-induced fumarate reduction was tested.13C5-glutamine tracing in SDHB-null RquA-expressing cells displayed less fumarate reduction and succinate oxidation than the RquA-expressing cells (Figures 10D-10F). Moreover, RquA- expressing 143B cells treated with the SDH inhibitor malonic acid displayed less fumarate reduction and succinate oxidation (Figure 10G). Thus, RQ requires SDH to catalyze fumarate reduction.To corroborate that RQ drives fumarate reduction in an SDH-dependent manner, we performed an orthogonal1C4-aspartate tracing assay in which labeling into13C4-fumarate and13C4-succinate was monitored (Figure 2E). The ratio of %13C4-succinate : %13C4- fumarate and fraction13C4-succinate was higher in RquA-expressing cells than wild-type cells, and this was ablated in the RquA-expressing SDH-null cells (Figure 2G, Figure 10H).13C4-fumarate labeling was identical in each cell model (Figure 10H), demonstrating that RQ increases fumarate reduction without broadly driving labeling into the reductive arm of the TCA cycle.Additionally, fumarate reduction and succinate oxidation were monitored in purified mitochondria from wild-type and RquA-expressing cells (Figure 101). Fumarate reduction was proxied by monitoring succinate production over after initiating with fumarate andNADH. RquA-expressing mitochondria displayed a more NADH oxidation and fumarate reduction than wild-type cells (Figure 2H, Figure 10J). Succinate oxidation was proxied by monitoring fumarate production over time after initiating with succinate. Mitochondria from RquA-expressing cells performed less succinate oxidation (Figure 10K), consistent with RQ driving SDH reversal.RquA depletes UQ to make RQ, making the contribution of RQ production or UQ depletion to the phenotypes unclear. Thus, we synthesized two small molecule analogs of RQ designed to preserve the reduction potential and redox capabilities of RQ while enabling its uptake in cells (Figure 3A). RQ analogs HKJS-001 and HKJS-003 were structurally validated with1H-NMR and13C-NMR (Figures 11A-1 IE). Molecular docking analysis of RQ analogs, UQio, and RQio into human complex I (PDB: 5XTD), and human complex II (PDB: 8GS8) reveal that RQ analogs interact with similar affinities as UQ and RQ with the quinone binding pockets of complexes I and II (Figures 1 1F-11 G).HKJS-001 and HKJS-003 didn’t impact UQ levels or basal O2 consumption rate, but decreased O2 linked ATP production, spare respiratory capacity, and maximal respiration (Figures 11H-1 IN). Consistent with RQ analogs siphoning electrons onto fumarate as the electron acceptor via SDH,13Cs-glutamine tracing demonstrates that HKJS-001 and HKJS- 003 increase fumarate reduction in wild-type, but not SDHB knockout cells (Figures 3B- 3C). In contrast to the RquA model, HKJS-001 and HKJS-003 modestly reduced succinate oxidation (Figures 12A-12B). To rule out that the HKJS-003 triphenylphosphine moiety, which can uncouple the membrane potential, drives fumarate reduction, cells were treated with the uncoupler CCCP alone. CCCP didn’t impact fumarate reduction, demonstrating that HKJS-003 drives this reaction independently of the membrane potential (Figures 12C- 12D).The ability for RQ analogs to drive fumarate reduction was monitored using an orthogonal assay on purified mitochondria from wild-type and SDHB knockout 143B cells (Figure 3D). RQ analogs performed more NADH oxidation and fumarate reduction than vehicle treated wild-type mitochondria, but not SDH-null mitochondria (Figures 3E-3G, Figures 12E-12F). Thus, through delivery of RQ to cultured cells using both genetic and pharmacological tools, we establish that RQ carries electrons to fumarate, instead of O2, as the terminal electron acceptor via SDH.UQ and RQ support distinct programs of mitochondrial functionAs UQ and RQ direct electrons on distinct ETC paths, they may differentially regulate ETC-dependent mitochondrial functions. Metabolite profiling of 143B and Caki-1 cells using the UQ and RQ-directed ETCs revealed differences in amino acid, nucleotide, amino sugar, and tricarboxylic acid (TCA) cycle metabolites (Figure 4A, Figures 13A-13B).ATP synthesis at complex V is coupled to the proton motive force generated by complexes I, III, and IV. RQ circumvents complexes III and IV, and instead delivers electrons to fumarate via SDH, which does not pump protons. Given the lower E o of RQ, its ability to drive proton pumping by complex I is unclear. RquA expression reduced mitochondrial membrane potential and ATP:ADP ratio (Figures 4B-4C, Figure 13C), and CCCP further depolarized the membrane potential, suggesting RQ partially supports proton pumping by complex I. In RquA-expressing SDH-null cells, the ATP:ADP ratio was similar to that of the RquA-expressing line (Figure 4C), suggestive of metabolic rewiring to glycolysis-derived ATP to compensate for loss of mitochondrial ATP synthesis. Consistent with this, RquA-expressing cells proliferated in galactose slower than wild-type cells, and this proliferation defect was exacerbated in RquA-expressing SDH-null cells (Figure 4D, Figure 13D). As galactose is catabolized slower than glucose, generating less glycolysis- derived ATP and making cells more reliant on mitochondrial ATP, these data imply that the RQ / fumarate ETC can sustain low levels of mitochondrial ATP synthesis.The electron carrier facilitates NADH oxidation at complex I. Switching the electron carrier from UQ to RQ didn’t alter the NAD+:NADH ratio or impact the proliferation rate of cells in pyruvate-free media (Figures 13E-13F). As pyruvate-free media limits NADH oxidation by lactate dehydrogenase, forcing dependence on complex I for NADH oxidation, these data imply the RQ / fumarate ETC supports complex I-mediated NADH oxidation. Consistent with this, SDH-null RquA-expressing cells were less capable of proliferating in these conditions (Figure 13F). Moreover, lactate was unchanged in RquA-expressing cells but significantly elevated in RquA-expressing SDH-null cells (Figure 13G). As cells compensate for complex I inhibition by shunting pyruvate into lactate, these data imply that the RQ / fumarate ETC supports complex I activity.Dihydroorotate dehydrogenase (DHODH) catalyzes the oxidation of dihydroorotate to orotate during de novo pyrimidine synthesis. DHODH activity was measured using13C4- aspartate tracing into13Cs-UTP in wild-type and RquA-expressing cells, which equally labeled13Cs-UTP in a DHODH-dependent manner (Figure 4E).13C3-UTP labeling was significantly reduced in RquA-expressing SDH-null cells, demonstrating that RQ mustdeliver electrons to fumarate to sustain DHODH activity (Figure 4E). Orthogonally, cells using either electron carrier were capable of proliferating in uridine-free media in a manner ablated by brequinar (Figure 10H). RquA-expressing SDH-null cells were significantly less capable of proliferating in uridine- free media, corroborating the dependence on fumarate reduction to sustain de novo pyrimidine synthesis (Figure 10H) in the absence of exogenous uridine. Thus, UQ and RQ equally support de novo pyrimidine biosynthesis.RQ analogs operate in parallel to UQ, siphoning a fraction of the electrons onto fumarate. Thus, their impacts on mitochondrial functions are more subtle than RquA expression. Metabolomic analysis of cells treated with the RQ analog HKJS-001 revealed many significant changes in amino acids, amino sugars, and the TCA cycle (Figures 14A- 14B). HKJS-001 increased the succinate: fumarate ratio in an SDH-dependent manner (Figure 14C), and didn’t impact complex I-mediated NADH oxidation or DHODH- mediated pyrimidine synthesis (Figures 14D-14H). Upon HKJS-001 treatment, the ATP:ADP ratio trended, but was not significantly lower, however, the capacity to proliferate in galactose was significantly reduced (Figures 14I-14J).ETC-derived ROS are signaling metabolites. Complexes I and III generate superoxide that decomposes to hydrogen peroxide and subsequently water by glutathione peroxidases and glutathione S -transferases in a reaction linking two molecules of reduced glutathione (GSH), generating oxidized glutathione (GSSG). RquA-expressing cells, but not RquA-expressing SDH-null cells, had a higher GSH:GSSG ratio than wild-type cells (Figure 4F, Figure 14K), indicating lower levels of ROS in cells employing the RQ / fumarate ETC. Hydrogen peroxide and superoxide were also reduced in RquA- expressing cells (Figures 4G-4H). Similarly, the RQ analogs HKJS-001 and HKJS-003 elevated the GSH:GSSG ratio and lowered hydrogen peroxide and superoxide levels in an SDH-dependent manner (Figures 14L-14M). Notably, HKJS-001 is ~200x more potent and ~3x more powerful than N-acetyl cysteine at quenching ROS (Figure 14N). Thus, in bypassing complexes III and IV in the ETC, RQ drives lower mitochondrial ROS than UQ. Taken together, these data demonstrate that the electron carrier utilized can significantly impact mitochondrial functions in mammalian cells (Figure 41). The RQ / fumarate ETC generates less ATP and ROS than the UQ / O2 ETC while preserving de novo pyrimidine biosynthesis and NADH oxidation.Reprogramming the ETC to the RQ / fumarate pathway is protective in hypoxiaThe O2 content across mammalian tissues and within regions of a given tissue are highly variable. Because RQ directs electrons onto fumarate instead of O2, we considered that cells using the RQ circuit may be more resistant to these hypoxic niches (Figure 5A). Hypoxia damages mitochondria, leading to mitophagy. Upon culturing wild-type cells in 0.5% O2, TOM20 and NDUFB8, an outer mitochondrial membrane protein and component of complex I, respectively, were depleted (Figure 5B). Reprograming the ETC from the UQ / O2 to RQ / fumarate pathway protected cells from loss of mitochondrial content in hypoxia (Figure 5B). Notably, as RquA-expressing SDHB-null cells are incapable of proliferating in hypoxia (Figure 140), we could not test the SDH-dependence of this phenomenon.RNA sequencing analysis of wild-type and RquA-expressing cells cultured in atmospheric or 0.5% O2 revealed that the UQ / O2 or RQ / fumarate ETC induced the HIF transcriptional program to the same extent (Figures 15A-15D). Gene set enrichment analysis revealed many examples of RQ mitigating hypoxia-induced metabolic stress. For example, cells using the RQ / fumarate ETC induced glycolysis less than cells using the UQ / O2 ETC (Figure 15 A). RquA-expressing cells also displayed less of the G2M checkpoint hallmark in hypoxia, suggestive of better proliferation (Figure 15 A). RNA sequencing corroborated that RQ mitigates loss of mitochondrial content in hypoxia, as cells using the UQ-directed, but not RQ-directed ETC decreased the oxidative phosphorylation hallmark and most ETC subunits were preserved in RQ-utilizing cells (Figure 5C, 15 A- 151). Also, RquA-expressing cells displayed less induction of the mitochondrial unfolded protein response protein Lonpl (Figure 15E). Consistent with RNA sequencing results, reprogramming the ETC via RquA expression or treatment with RQ analogs suppressed hypoxia-induced proliferation defects (Figures 16A-16C). Moreover, UQ-utilizing cells increase glucose consumption and lactate synthesis to compensate for decreased NADH oxidation and ATP production by the ETC in hypoxia. Reprogramming the ETC to the RQ / fumarate pathway blocked these metabolic adaptations (Figures 5D-5E). Thus, RQ mitigates metabolic stress and loss of mitochondrial content in hypoxia.ROS are byproducts of the ETC upon hypoxia and O2 reperfusion. To clear ROS, cells decrease the GSH:GSSG ratio, suggestive of ROS buildup and turnover in 0.5% O2 (Figure 5F). As ROS are generated by complexes I and III, and RQ circumvents complex III in the ETC, we tested if reprograming the ETC from the UQ to RQ pathway impacts hypoxia-induced ROS. Indeed, cells using the RQ-directed ETC via RquA expression andHKJS-001 treatment displayed a higher GSH:GSSG ratio than cells using the UQ-directed ETC in hypoxia (Figure 5F, Figure 16D). Moreover, cells using the RQ / fumarate ETC had lower superoxide and hydrogen peroxide in both chronic and acute hypoxia (Figures 5G-5J, Figures 16E-16G). Thus, RQ protects cells from ROS accumulation in hypoxia.Reprogramming the ETC mitigates ischemia reperfusion injuryWe next sought to determine if RQ carries electrons to fumarate as an electron acceptor in vivo. Since the mammalian RQ biosynthetic pathway is unknown, lowering RQ in vivo isn’t yet possible. Therefore, we leveraged our genetic and pharmacologic tools to elevate RQ levels in vivo. Mice were infected with adeno-associated virus 9 (AAV9) to induce expression of either mCherry or RquA in mouse liver, changing the ratio of RQ:UQ from 1 :100 to 200:1, effectively swapping the electron carrier upon RquA expression (Figures 6A-6B, Figures 17A-17B). Remarkably, although RquA expression reduced UQ in the liver by -90%, mice appeared healthy and didn’t exhibit any noticeable phenotypes consistent with mitochondrial dysfunction, suggesting RQ could sustain the ETC in physiological contexts.To test if RQ carries electrons to fumarate in vivo, we performed13Cs-glutamine tracing in these mice. Elevating RQ in the liver via RquA expression not only increased fumarate reduction but also labeling in the entire reductive carboxylation pathway (Figure 6C). Specifically,13Cs-glutamine incorporation into13Cs -citrate,13C3 -malate,13C3 - fumarate, and13C3 -succinate was higher in the RquA-expressing livers (Figure 6C). We next tested how RQ impacts mitochondrial functions in vivo. Consistent with our data in vitro, swapping UQ with RQ via RquA expression significantly increased the GSH:GSSG ratio, suggestive of less oxidative stress (Figure 6D). Moreover, since RQ bypasses the proton pumping complexes III and IV, and instead delivers electrons to fumarate via complex II, RquA expression decreased the ATP:ADP ratio (Figure 6E). Beyond ATP and GSH levels, RquA expression in the liver altered amino sugar, nucleotide, and arginine and proline metabolism (Figures 17C-17D). Thus, reprogramming the ETC in the liver reveals that RQ can deliver electrons to fumarate as the electron acceptor and alter mitochondrial functions in ATP and ROS production.As RquA increases RQ while decreasing UQ, we sought to corroborate the ability for RQ to carry electrons in the ETC with an orthogonal approach. Mice were injected with the RQ analog HKJS-001, which accumulated in the liver, and then were subjected to13Cs- glutamine tracing to monitor fumarate reduction (Figures 17E-17F). Consistent with RQpromoting the use of fumarate as an electron acceptor via SDH, treatment with the RQ analog HKJS-001 increased labeling into ' ’C vsuccinate in a manner suppressed by malonic acid (Figure 6F, Figure 17G). Similar to RquA expression, HKJS-001 treatment increased labeling in the reductive arm of the TCA cycle as depicted by increasedBCF -fumarate,nCF -malate, and13Cs-citrate, in a SDH-dependent manner (Figure 6F, Figures 17G-17J). Thus, RQ delivers electrons to fumarate as the electron acceptor via SDH in vivo.Reprogramming the ETC to the RQ / fumarate pathway in vitro protected cells from metabolic stress in hypoxia. Modeling hypoxia in vitro does not recapitulate all the features of physiological hypoxia, especially considering the extent and duration of O2 deprivation, the simultaneous restriction of nutrients that coincides with limited vascularization, and the gradual O2 reperfusion. To test if reprogramming the ETC via RQ impacts tissue sensitivity to hypoxia we used a hindlimb ischemia (HLI) model, in which the femoral artery is ligated in one leg while keeping the other leg as a healthy control. Mice were prophylactically injected mice with either vehicle or the RQ analog HKJS-001, HLI was induced, and gastrocnemius muscles were dissected 2 and 24 hours later from healthy and ischemic legs (Figure 6G). Ischemia robustly triggers oxidative stress during both the initial hypoxia, and upon reperfusion of blood flow driving reverse electron transfer (RET) and superoxide production. Consistent with HLI-induced oxidative stress, vehicle, but not HKJS-001 treated mice displayed a reduction of GSH:GSSG by 24 hours after HLI (Figure 6H). This ratio was driven by a decrease in GSH, but not GSSG, in the muscle (Figures 17K-17L). To further probe whether HKJS-001 impacts tissue recovery from HLI, we monitored blood flow to the hindlimb for up to 28 days, when mice fully recovered from the injury (Figures 17M-17N). Remarkably, although vehicle and HKJS-001 treated mice displayed equal ablation of blood flow to their hindlimb at day 0, the HKJS-001 treated mice recovered 2- fold quicker (Figures 6I-6J). We speculate that this acceleration of recovery could be caused by RQ-mediated suppression of oxidative stress impacting c-Jun NH2 terminal kinase (JNK) signaling to promote recovery of vasculature, or by suppressing hypoxia-induced mitochondrial membrane potential depolarization by priming the tissue to utilize the RQ / fumarate ETC. Thus, the RQ analog HKJS-001 protects against oxidative damage upon ischemia reperfusion injury, and consequently accelerates the rate of tissue recovery.DiscussionHere, we identify RQ as an electron carrier for the mammalian ETC present in certain tissues and absent from cells cultured in vitro. RQ has a lower E 0 than UQ, enablingit to favorably deliver electrons to fumarate as the terminal electron acceptor via reversal of SDH, independently of environmental O2 levels. Through expression of the bacterial enzyme RquA, which converts UQ to RQ, and development of RQ analogs, we establish methods to reprogram electron flow in the mammalian ETC to the RQ / fumarate pathway. Reprogramming the ETC mitigates hypoxia-induced metabolic stress in vitro and in vivo. Thus, we establish an Ch-independent node of flexibility in the mammalian ETC that can be leveraged to ameliorate hypoxia-related ailments. We speculate that distinct ETC pathways, which differentially impact mitochondrial functions, serve specific physiological roles. For example, as the brain experiences intermittent periods of hypoxia, utilization of the RQ- directed ETC may mitigate damage that could be caused by fluctuating O2 levels. The UQ- directed ETC may be favored in tissues such as the heart and skeletal muscle, which rely on high levels of ATP to sustain cycles of contraction and relaxation.A thermodynamic perspective of RQ in the mammalian ETCFor an electron carrier to transport electrons within the ETC, it must have a reduction potential greater than the electron donor, and lower than the electron acceptor. RQ (E 0 -63 mV) accepts electrons from NADH (E 0 -320 mV) and donates them to fumarate (E 0 +30 mV). Theoretically, RQ should also be capable of delivering electrons to cytochrome C (E 0 +254 mV) via complex III, which would ultimately deliver these electrons to O2 (E 0 +820 mV) via complex IV. However, our findings indicate that RQ does not drive O2 reduction. First, RquA expression, which converts UQ to RQ, decreases complex III and IV activities. Second, hypoxia does not drive RQH2 accumulation, implying that O2 does not contribute to RQH2 oxidation. Third, cells relying on RQ without SDH activity exhibit mitochondrial dysfunction, including impaired pyrimidine synthesis, lactate buildup, and reliance on glycolysis for ATP. If RQ could deliver electrons to O2, SDH knockout would be compensated for by delivery of electrons to O2 instead. Data on the cytochrome bm complex in yeast demonstrate that RQH2 drives less cytochrome bm complex activity than UQH2 and is uninhibited by antimycin A. As antimycin inhibits this complex by binding the Qi pocket, these data imply RQH2 has a weak affinity for the Qi pocket of complex III. Thus, through likely substrate selectively for UQH2 at complex III, RQH2 preferentially deposits its electrons onto fumarate at complex II.Another intriguing thermodynamic phenomenon is the ability for RQ to catalyze complex I-mediated NADH oxidation. While UQ drives complex I activity with a massiveAE o of +420 mV, enabling proton pumping, the AE o between NADH and RQ (+257 mV), is also favorable, but may not liberate enough energy to facilitate proton pumping. Further studies will need to be performed to quantify how much RQ contributes to the proton gradient. Additionally, whether RQ can support other ETC-dependent mitochondrial functions such as H2S oxidation, fatty acid oxidation, and proline catabolism, requires future investigation.Therapeutic implications of reprogramming the ETCOur discovery of RQ in certain mammalian tissues inspired the development of genetic and pharmacologic tools that reprogram electron flow to the RQ / fumarate ETC in vitro and in vivo. Using these tools, we find that reprogramming the ETC via RQ or its mimetics mitigate hypoxia-induced mitochondrial turnover, metabolic, and oxidative stress. Interestingly, exogenous supplementation of Vitamin K2 (menaquinone), has been shown to mitigate mitochondrial dysfunction, and minimize Ap42-induced neurotoxicity in flies. Whether these effects are caused by Vitamin K2-induced and SDH-mediated fumarate reduction isn’t yet known. Collectively, these data point to the potential for future development of other synthetic electron carriers that can similarly divert electron flow in the ETC to treat mammalian diseases caused by hypoxia or ETC dysfunction including mitochondrial myopathies, cancer, diabetes, obesity, pulmonary disease, and sickle cell anemia.Ischemia reperfusion injury is a potential clinical application of RQ-mediated ETC reprogramming. ROS in ischemia reperfusion injury can accumulate due to hypoxia caused by restricted blood flow, leading to complex Ill-derived ROS, and RET at complex I upon reperfusion of blood flow. In bypassing complexes III and IV, RQ mitigates complex Ill- derived ROS in hypoxia. Moreover, as RQ promotes the reverse, fumarate reductase activity of the SDH complex, RQ likely reduces succinate oxidation upon O2 reperfusion, which is the main source of electron input for RET during ischemia reperfusion injury. Moreover, it is unclear if RQH2 can drive reversal of complex I, as there is a steep thermodynamic barrier to complex I reversal that requires UQH2 buildup and depolarization of the membrane potential. Given that hypoxia does not cause RQH2 buildup, it is possible that RQ drives lower RET than UQ during ischemia, contributing to its protective effects. Finally, as RQ provides a selective advantage for proliferating cells in hypoxia, a potential drawback of therapeutically reprograming the ETC is supporting the growth of tumors.Although we never detected any cancer in our mice treated with RQ analogs and upon RquA-expression, future studies will test the safety of this therapeutic strategy.Tissue, cell type, and regional specificity of the RQ / fumarate ETCUnlike UQ, which is ubiquitous across mammalian tissues, the levels of RQ are variable and significantly lower than UQ. Understanding the mechanisms underlying RQ tissue distribution will be critical to elucidating its physiological function in mammals. One interesting hypothesis is that RQ is enriched in specific cells within tissues that require less mitochondrial-derived ROS and ATP. Certainly flux through the mitochondrial TCA cycle is cell-type dependent, and the same is likely true of electron flow in the ETC. Another hypothesis is that RQ is enriched in hypoxic tissue niches, such as the gastrointestinal tract and renal medulla, to support mitochondrial functions. Additionally, future studies will elucidate if a given mitochondrion can have both UQ and RQ simultaneously, or if UQ and RQ are present in distinct mitochondrial populations. Finally, working out the mammalian RQ biosynthetic pathway will significantly advance our understanding of the tissue, cell type, and regional specificity of this pathway.There are likely multi-tiered regulatory mechanisms of ETC pathway selection in mammalian cells. For example, the liver, which catalyzes fumarate reduction, does not have high levels of RQ, but has significant UQEF accumulation, likely driving fumarate reduction in this context. Beyond UQFE accumulation, complex II reversal can be regulated by the levels of succinate and fumarate, local pH, and other mitochondrial metabolites that block electron transfer to O2, forcing cells to employ fumarate as the electron acceptor instead. For example, hydrogen sulfide (H2S) inhibits complex IV at high concentrations, enabling UQH2 buildup and fumarate reduction. To best understand how ETC circuits are regulated in physiological contexts, each of these factors will need to be considered in each tissue.Evolutionary conservation of electron carriersFlexibility in the ETC is a highly conserved phenomenon. Other electron carriers, including RQ, persist in bacterial and eukaryotic evolutionary lineages. The RQ biosynthetic pathways differ between bacteria and C. elegans, and our data indicate additional divergence in the biosynthetic pathway within the eukaryotic lineage, as the isoform of coq-2 required for C. elegans to synthesize RQ isn’t present in mammals. Thus, anti-parasitic agents targeting the RQ biosynthetic pathway are not likely to interfere with mammalian RQ synthesis, providing a therapeutic window to selectively target RQ inpathogens to treat infection. Understanding the RQ biosynthetic pathway in mammals will be of utmost importance for understanding its evolutionary origins.Limitations of studyThe mammalian RQ biosynthetic pathway remains unknown, preventing in vivo studies that deplete RQ, limiting insights into its physiological role in mammals. Without such tools, the interplay between UQ and RQ cannot be fully understood, including whether UQ and RQ coexist in the same cells or mitochondria and whether UQ and RQ shuttle electrons between each other. Throughout the study, LC-MS was used to measure RQ, relying on purified standards for the expected mass, adducts, and retention times. However, mass spectrometry cannot resolve the precise structural arrangement of the functional groups on the RQ benzenic ring; future NMR studies are needed for this purpose. Additionally, isotopologue ratios to infer SDH activities are confounded by changes in metabolite pool size, enzyme exchange rates, and interference with gluconeogenesis that complicate interpretations of glutamine tracer data. Despite these limitations, our findings that RQ promotes fumarate reduction in mammalian mitochondria are supported by orthogonal assays including stable isotope tracers, SDH knockouts, and purified mitochondria.References1. Spinelli, J.B., and Haigis, M.C. (2018). The multifaceted contributions of mitochondria to cellular metabolism. Nat Cell Biol 20, 745-754.2. Martinez-Reyes, I., and Chandel, N.S. (2020). Mitochondrial TCA cycle metabolites control physiology and disease. Nat Commun 11, 102.3. Osellame, L.D., Blacker, T.S., and Duchen, M.R. (2012). Cellular and molecular mechanisms of mitochondrial function. Best Pract Res Clin Endocrinol Metab 26, 711-723.4. Spinelli, J.B., Rosen, P.C., Sprenger, H.G., Puszynska, A.M., Mann, J.L., Roessler, J.M., Cangelosi, A.L., Henne, A., Condon, K.J., Zhang, T., et al. (2021). Fumarate is a terminal electron acceptor in the mammalian electron transport chain. Science 374, 1227- 1237.5. Monzel, A.S., Enriquez, J.A., and Picard, M. (2023). Multifaceted mitochondria: moving mitochondrial science beyond function and dysfunction. Nat Metab 5, 546-562.6. Alberts B, J.A., Lewis J, et al. (2002). Electron-Transport Chains and Their Proton Pumps. Molecular Biology of the Cell. 4th edition.7. Alberts B, J.A., Lewis J, et al. Garland Science (2002). Electron-Transport Chains and Their Proton Pumps. Molecular Biology of the Cell. 4th edition.8. Becucci, L., Lottini, E., and Guidelli, R. (2011). Influence of gel-phase microdomains and lipid rafts in lipid monolayers on the electron transfer of a lipophilic redox probe: dioctadecylviologen. Physical Chemistry Chemical Physics 13, 3917-3924.9. Becucci, L., Scaletti, F., and Guidelli, R. (2011). Gel-phase microdomains and lipid rafts in monolayers affect the redox properties of ubiquinone- 10. Biophys J 101, 134-143.10. Rutter, J., Winge, D.R., and Schiffman, J.D. (2010). Succinate dehydrogenase - Assembly, regulation and role in human disease. Mitochondrion 10, 393-401.11. Kumar, R., Landry, A.P., Guha, A., Vitvitsky, V., Lee, H.J., Seike, K., Reddy, P., Lyssiotis, C.A., and Banerjee, R. (2022). A redox cycle with complex II prioritizes sulfide quinone oxidoreductase-dependent H(2)S oxidation. J Biol Chem 298, 101435.12. Hubbard, B.T., LaMoia, T.E.„ and Goedeke, L., Gaspar, R.C., Galsgaard, K.D., Kahn, M., Mason, G.F., Shulman, G.I (2023). Q-Flux: A method to assess hepatic mitochondrial succinate dehydrogenase, methylmalonyl-CoA mutase, and glutaminase fluxes in vivo. Cell Metabolism 35, 212-226.13. Chinopoulos, C. (2019). Succinate in ischemia: Where does it come from? Int J Biochem Cell Biol 115, 105580.14. Chouchani, E.T., Pell, V.R., Gaude, E., Aksentijevic, D., Sundier, S.Y., Robb, E.L., Logan, A., Nadtochiy, S.M., Ord, E.N.J., Smith, A.C., et al. (2014). Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS. Nature 515, 431-435.15. Bisbach, C.M., Hass, D.T., Robbings, B.M., Rountree, A.M., Sadilek, M., Sweet, I.R., and Hurley, J.B. (2020). Succinate Can Shuttle Reducing Power from the Hypoxic Retina to the O(2)-Rich Pigment Epithelium. Cell Rep 31, 107606.16. Tielens, A.G.M., Van Hellemond , J.J (1998). The electron transport chain in anaerobically functioning eukaryotes. Biochimica et Biophysica Acta 1365, 71-78.17. Harsh R. Pershad, J.H., Bruce Cochran, Brian A.C. Ackrell,, and Armstrong, F.A. (1999). Voltammetric studies of bidirectional catalytic electron transport in Escherichia coli succinate dehydrogenase: comparison with the enzyme from beef heart mitochondria, biochemica et biophysica acta 1412, 262-272.18. Keeley, T.P., and Mann, G.E. (2019). Defining Physiological Normoxia for Improved Translation of Cell Physiology to Animal Models and Humans. Physiol Rev 99,19. Krab, K., Kempe, H., and Wikstrom, M. (2011). Explaining the enigmatic K(M) for oxygen in cytochrome c oxidase: a kinetic model. Biochim Biophys A...

Claims

WHAT IS CLAIMED IS:

1. A compound defined by Formula I or Formula II belowor a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, whereinZ is chosen from, C<)-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce -24 alkoxy, Ce 24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1 , 2, or 3 independently selected RAgroups;R1is chosen from Ci-Ce alkyl and Ci-Ce haloalkyl;R2and R2are independently chosen from hydrogen, Ci-Ce alkyl, and Ci-Ce haloalkyl, or R2and R2, together with the nitrogen atom to which they are attached, combine to form a 3 to 7 membered heterocycloalkyl ring;R3is chosen from hydrogen, Ci-Ce alkyl, and Ci-Ce haloalkyl;L is absent, or represents a bivalent linking group;A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, CM haloalkyl, Ci-6 alkoxy, C 1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-e alkyl)amino, thio, Ci-e alkylthio, C 1-6 alkylsulfinyl, C1-6 alkylsulfonyl, carbamyl, C 1-6 alkylcarbamyl, di(Ci-6 alkyl )carbamyl, carboxy, Ci-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, Ci -6 alkylaminosulfonylamino, di(Ci-6 alkyl)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.

2. The compound of claim 1 , wherein R1is methyl.

3. The compound of claim 1, wherein R1is CF3.

4. The compound of any of claims 1-3, wherein R2and R2are hydrogen.

5. The compound of any of claims 1-4, wherein R3is methyl.

6. The compound of any of claims 1-4, wherein R3is CF3.

7. The compound of any of claims 1-6, wherein Z is Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkyl cycloalky], Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups.

8. The compound of claim 7, wherein Z is Ce-24 alkyl optionally substituted by 1, 2, or 3 independently selected RAgroups.

9. The compound of claim 7, wherein Z is Ce-24 alkylaryl optionally substituted by 1, 2, or 3 independently selected RAgroups.

10. The compound of any of claims 1-6, wherein Z is11. The compound of claim 10, wherein L is absent.

12. The compound of claim 10, wherein L is a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms.

13. The compound of claim 12, wherein L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.

14. The compound of claim 12, wherein L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.

15. The compound of any of claims 10-14, wherein the mitochondrial targeting moiety comprises a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof.

16. The compound of claim 15, wherein the mitochondrial targeting moiety comprises a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation.

17. The compound of claim 15, wherein the mitochondrial targeting moiety comprises a Szeto-Shiller peptide.

18. The compound of claim 1 , wherein the compound is defined by Formula IA orFormula IIA belowor a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, whereinZ is chosen from, Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups;L is absent, or represents a bivalent linking group;A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C 1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-6 alkyl)amino, thio, C1-6 alkylthio, C 1-6 alkylsulfinyl, C1-6 alkylsulfonyl, carbamyl, C 1-6 alkylcarbamyl, di(C 1-6 alky l)carbamyl, carboxy, C1-6 alkylcarbonyl, C 1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, Ci-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino,C1-6 alkylaminosulfonylamino, di(C 1-6 alky l)aminosulfonylamino, aminocarbonylamino, Ci-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.

19. The compound of claim 1, wherein the compound is defined by Formula IB orFormula IIB belowFormula IB Formula IIB or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, whereinZ is chosen from, Ce-24 alkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, G, 24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups;L is absent, or represents a bivalent linking group;A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Cue alkoxy, C 1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(C 1-6 alky l)amino, thio, C1-6 alkylthio, C 1-6 alkylsulfinyl, C1-6 alkylsulfonyl, carbamyl, C 1-6 alkylcarbamyl, di(Ci-6 alkyl)carbamyl, carboxy, Cue alkylcarbonyl, C 1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, C1-6 alkylaminosulfonylamino, di(C 1-6 alky l)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-6 alkyl)aminocarbonylamino.

20. The compound of claim 1 , wherein the compound is defined by Formula IC orFormula IIC belowFormula IC Formula IIC or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, whereinL is chosen from, Ce-24 alkyl, Ce-24 alkynyl, Co-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups;L is absent, or represents a bivalent linking group;A represents a mitochondrial targeting moiety; and each RAis independently selected from OH, NO2, CN, halo, Ci e alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, C1-6 alkoxy, C 1-6 haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, C 1-6 alkylamino, di(Ci-e alkyl)amino, thio, Ci-6 alkylthio, C 1-6 alkylsulfinyl, Ci-6 alkylsulfonyl, carbamyl, C 1-6 alkylcarbamyl, di(Ci-6 alkyl)carbamyl, carboxy, C1-6 alkylcarbonyl, C1-6 alkoxycarbonyl, C1-6 alkylcarbonylamino, C 1-6 alkylsulfonylamino, aminosulfonyl, C 1-6 alkylaminosulfonyl, di(Ci-6 alkyl)aminosulfonyl, aminosulfonylamino, C1-6 alkylaminosulfonylamino, di(C 1-6 alky l)aminosulfonylamino, aminocarbonylamino, C1-6 alkylaminocarbonylamino, and di(Ci-e alkyl)aminocarbonylamino.

21. The compound of any one of claims 18-20, wherein Z is Ce-24 alkyl, Ce-24 heteroalkyl, Ce-24 alkynyl, Ce-24 haloalkyl, Ce-24 alkoxy, Ce-24 haloalkoxy, Ce-24 alkylcycloalkyl, Ce-24 alkylhetercycloalkyl, Ce-24 alkylaryl, and Ce-24 alkylheteroaryl, each optionally substituted by 1, 2, or 3 independently selected RAgroups.

22. The compound of claim 21, wherein Z is Ce-24 alkyl optionally substituted by 1, 2, or 3 independently selected RAgroups.

23. The compound of claim 21, wherein Z is Ce-24 alkylaryl optionally substituted by 1, 2, or 3 independently selected RAgroups.

24. The compound of any of claims 18-20, wherein Z is25. The compound of claim 24, wherein L is absent.

26. The compound of claim 24, wherein L is a linking group comprising from 3 to 200 atoms, such as from 6 to 50 atoms.

27. The compound of claim 26, wherein L represents a C3-18 alkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.

28. The compound of claim 26, wherein L represents a C3-18 heteroalkylene group optionally substituted by 1, 2, or 3 independently selected RAgroups.

29. The compound of any of claims 24-28, wherein the mitochondrial targeting moiety comprises a lipophilic cation, a mitochondrial targeting sequence, or a combination thereof.

30. The compound of claim 29, wherein the mitochondrial targeting moiety comprises a lipophilic cation chosen from a triphenylphosphonium (TPP) cation or a rhodamine cation.

31. The compound of claim 29, wherein the mitochondrial targeting moiety comprises a Szeto-Shiller peptide.

32. The compound of any of claims 1-31, wherein the compound comprises one of the following:wherein n is an integer from 3 to 18, Ph represents phenyl, and TPP represents a triphenylphosphonium cation.

33. A pharmaceutical composition comprising therapeutically effective amount of a compound of any of claims 1-32.

34. The pharmaceutical composition of claim 33, wherein the therapeutically effective amount of the compound of any of claims 1-32 is encapsulated in a liposome or lipid nanoparticle.

35. A method of treating a disease in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of any of claims 1-32, wherein the disease is a mitochondrial disorder, a metabolic disorder, a disorder that induces or results from oxidative stress, an oxygen free radical disorder including a hypoxia related disease, inflammation, or a disease resulting from rhodoquinone depletion.

36. The method of claim 35, wherein the subject is a mammal, such as a human.

37. The method of any of claims 35-36, wherein the disease is a metabolic disorder.

38. The method of any of claims 35-37, wherein the disease is obesity.

39. The method of any of claims 35-37, wherein the disease is diabetes.

40. The method of any of claims 35-36, wherein the disease is ischemia.

41. The method of any of claims 35-36 or 40, wherein the ischemia is ischemia of the pancreas, adipose tissue, skeletal muscle, brain, kidney, liver, gastrointestinal tract, heart, or lung.

42. The method of any of claims 35-36, wherein the disease is hypoxia.

43. The method of any of claims 35-36 or 42, wherein the disease is exercise-induced hypoxia.

44. The method of any of claims 35-36 or 42, wherein the disease is hypoxia resulting from ischemia.

45. The method of any of claims 42-44, wherein the hypoxia is hypoxia of the heart.

46. The method of any one of claims 42-44, wherein the hypoxia is hypoxia of the lung.

47. The method of any of claims 35-36, wherein the disease is oxidative stress.

48. The method of any of claims 35-36, wherein the disease is a neuromuscular disorder.

49. The method of claim 48, wherein the neuromuscular disorder is a mitochondrial myopathy.

50. The method of any of claims 35-36, wherein the disease is a neurodegenerative disorder.

51. The method of claim 50, wherein the neurodegenerative disorder results from mutations in the mitochondrial DNA.

52. The method of any of claims 35-36, wherein the disease is CoQ-10 deficiency.

53. The method of any of claims 35-36, wherein the disease is mitochondrial complexIll deficiency.

54. The method of any of claims 35-36, wherein the disease is mitochondrial complex IV deficiency.

55. The method of any of claims 35-36, wherein the disease is a proliferative disease.

56. The method of claim 55, wherein the proliferative disease comprises cancer, such as renal cell carcinoma.

57. The method of any of claims 35-36, wherein the disease is an inflammatory disease.

58. The method of any of claims 35-57, wherein the method further comprises administering an additional active agent to the subject.

59. The method of claim 58, wherein the additional active agent is chosen from a vitamin, an antioxidant, an antiinflammatory, an anti-cancer agent, an anti-obesity agent, a probiotic, an antibiotic, a statin, or a plasmid (e.g., a plasmid encoding a protein (e.g., an enzyme enabling in vivo conversion of ubiquinone to rhodoquinone (e.g., RquA))), or a combination thereof.

60. A method of reducing oxidation and / or oxidative stress in a biological sample, the method comprising contacting the biological sample with a compound of any of claims 1 - 32.

61. A method for reducing or preventing oxidation in a composition, the method comprising contacting the composition with a compound of any of claims 1-32.

62. The method of claim 61, wherein the composition comprises a food, a nutrient, a chemical, a pharmaceutical agent, a polymer, a biological sample, a protein, or a nucleic acid.

63. The use of a compound of a compound of any of claims 1-32 for the treatment of a disease in a subject in need thereof, wherein the disease is a metabolic disorder, hypoxia related disease, or a disease resulting from rhodoquinone depletion.64 The use of a compound of a compound of any of claims 1-32 as an antioxidant or preservative.

65. The use of a compound of a compound of any of claims 1-32 as a nutritional supplement.

66. The use of a compound of a compound of any of claims 1-32 ex vivo to prevent oxidative and / or oxidative stress in a biological sample, such as blood, tissue, and / organs in storage and / or blood, tissue, and / organs before and / or during transplantation.

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