AU2008354009A1 - Pharmaceutical composition - Google Patents

Description

WO 2009/123597 PCT/US2008/004410 1 Pharmaceutical Composition Field of the Invention This invention relates to therapeutic and diagnostic compositions, and more 5 particularly to pharmaceutical compositions, and methods of use thereof, which demonstrate selective uptake into cells characterized by hyperproliferation, including cancer cells, and which modulate the regulation or perturbation of the structure, expression, and/or activity of enzymes, thereby facilitating the detection and treatment or destruction of these cells. More specifically, these agents target and perturb the activity or regulation thereof of the altered 10 mitochondrial energy metabolism observed in such locales as the modified pyruvate dehydrogenase (PDH) complex associated with most cancers. Background of the Invention Mitochondria are the primary control centers for energy production and cellular life 15 and-death processes in eukaryotes. While various mechanisms of communication with the rest of the cell exist, reversible phosphorylation is an important means of regulating mitochondrial functions. (Pagliarini D.J. and Dixon J.E. (2006). Mitochondrial modulation: reversible phosphorylation takes center stage? TRENDS in Biochem. Sci. 31:26-34, passim, herein incorporated by reference) The steadily increasing number of reported mitochondrial 20 kinases, phosphatases, and phosphoproteins suggests that phosphorylation is likely to emerge as a common theme in the regulation of mitochondrial processes. Pathological or genetic changes associated in mitochondrial enzyme structure, function and activity regulation contribute to, and may be important targets for, the treatment of disease. In line with their role as both a point of convergence and regulator of diverse cellular 25 functions, mitochondria have crucial roles in apoptosis, production of reactive oxygen species (ROS), and numerous metabolic processes, including the production of more than 90% of WO 2009/123597 PCT/US2008/004410 2 cellular ATP. Furthermore, as cells grow and divide, new mitochondria have to be made, this process itself requiring careful coordination of nuclear and mitochondrial DNA transcription and translation. Finally, as cellular energy needs change, mitochondria must respond rapidly by tuning their ATP output. Hence, mitochondria require a complex system of 5 communication with cellular functions. As evident from FIGURE 1, signal molecules to and from mitochondria include ions, gases, metabolites, hormones, transcription factors and proteins. Consequently, the recognition of mitochondria as centers for receiving, integrating, and transmitting cellular signals is an important advance in the design and testing of pharmaceuticals. 10 A cornerstone of signalling in mitochondrial regulation is reversible phosphorylation. However, while the first demonstration of a protein kinase event was reported in 1954, and the fact that a core mitochondrial function can be regulated by reversible phosphorylation was discovered nearly four decades ago, reports of mitochondrial phosphorylation events are scarce. This is so despite the recognition in the 1980s and 1990s of numerous signal 15 transduction phosphorylation cascades that traverse the plasma membrane and extend through the cytosol to the nucleus. Such paucity of knowledge may be due partly to the fact that the bulk of the mitochondrial protein machinery lies behind two lipid bilayers, which seemingly places mitochondrial proteins out of the reach of cytosolic signalling cascades. In any event, it has been not widely accepted that the mitochondrion regulates signalling by reversible 20 phosphorylation in a manner key to disease management. Nevertheless, as seen in Table 1, by 2006 more than 60 proteins in all mitochondrial compartments (i.e., the matrix, inner membrane, intermembrane space, and outer membrane, including the cytoplasmic-facing outer surface) had been identified as phosphoproteins implicated in a wide spectrum of mitochondrial functions. Mounting data further demonstrates the importance of reversible WO 2009/123597 PCT/US2008/004410 3 phosphorylation of mitochondrial targets and the use of compositions targeting the same for the improved treatment of cancer. Table 1. Mitochondrial phosphoproteinsa No. Protein Location P site Source Function Refs 1 POC Ela M Ser Various Acetyl-CoA formation [11] 2 PDC E10 M Tyr Human sperm Acetyl-CoA formation [8] 3 PDC E3 M Tyr Hamster sperm Regulation of the PDC [8. 4 PDK isoform 2' M Ssr/Thr Rat TCA. [271 5 Aconitase M ? Bovine/potato TCA [22) 6 NAD-isocitrate dehydrogenase M .? Bovine/potato TCA [221 7 NAD-malate dehydrogenase M ? Potato TCA [221 q NAD-malic enzyme M ? Potato TCA [22] 9 Succinyl-CoA-ligase a subunit M ? Rat/potato- TCA [22.471 10 Succinyl-CoA-ligase 0 subunit M ? Rat/potato TCA [22,471 11 Formate dehydrogenase M Ser/Thr Potato TCA [22,23] 12 Aconitase M Tyr Guinea pig synaptosomes TCA .18] 13 BCKAD M Ser Various AA metabolism [31] 14 BCKAD kinase M Ser Rat AA Metabolism [54) 15 HSP22 M Ser -Corn Chaperone [39) 16 HSP 90 M ? Potato Chaperone. [22] 17 Chaperonin 60 M 7 Potato Chaperone (22] 18 mthsp75 M Tyr Rat hepatome cells Chaperone [29] 19 TRAP-1i M Tyr Human sperm Chaperone [8] 20 CYP2E1' M/IM? Sar COS Detoxification [43] 21 CYP2B1" M/IM? Ser COs Detoxification [181 22 GSTA 4-4 M Ser/Thr COS Detoxification 144] 23 DBP M ? Yeast mR NA turnover (383 24 MnSOD M ? Potato Oxidative stress defense [22) 25 EF-Tu M Thr? Rabbit heart Protein synthesis (321 26 Creatine kinase M 7 Bovine Synthesis of phosphocreatine [45 27 MTERF- M ? Rat Transcription termination [42] 28 Abf2p M Ser/Thr? Yeast mtDNA maintenance [26] 29 MtTBPb M ? Yeast mtDNA maintenance [501 30 NOK M/iMS Ser/His Pisum sativum Nucleoside triphosphate balance [49] 31 StAR IMS Ser COS-1 Steroid hormone synthesis [19) 32 Axmito" M? Tyr Rat Regulation of PLAs? [53 33 SSATti M? Ser? Rat Acetylation of spermidine [21] 34 Sab OM Ser Rat cardiac myocytes SH3 domain-binding protein [28] 35- CPT-i OM Ser Rat -.- OX [35 36 MtGAT* OM Ser/Thr? Rat Glycerolipid biosynthesis [411 37 BAD' GM Ser FLS.12 cells Apoptosis [30) 38 BCL-2 OM Ser Jurkat Apoptosis [17.521 39 BcI-xL OM Thr U-937 cells Apoptosis 36) 40 CREB M/IM Ser? . Rat mtDNA transcription? [24] 41 VDAC OM Tyr . Guinea pig synaptosomes transport [8,451 42 Ci: ESSS IM Ser Bovine OXPHOS [25) 43 Cl: 10 kDa IM Ser Bovine . OXPHOS [25] 44 C 42 kOa (2 sites) IM Ser & Thr Bovine OXPHOS [45,55 45 Ciii core I IM Tyr Human sperm OXPHOS (8} 46 Ciii core l IM ? Bovine OXPHOS- [45] 47 CIV I IM . Tyr Bovine OXPHOS [37] 48 CIV 1I IM Tyr Osteoclasts OXPHOS [40] 49' CIV Il1 IM Ser/Thr? Bovine OXPHOS [34] 50 CIV IV IM ? Rat OXPHOS [46] 51 CIV Vb" IM Ser/Thr? Bovine OXPHOS [34] 52 CV 1 IM ? Bovine/potato OXPHOS [22 53 CV 0 IM Thr Human sk mus/bovine OXPHOS [331 54 CV 5 IM ? Potato OXPHOS [48 55 CV b IM ? Potato -OXPHOS [48 56 ScIRP IM ? Rat OXPHOS [201 57 SDH-Fp IM 7 Bovine/potato. OXPHOS 1221 58 bcl complex, P-MPP subunit IM 7 Potato OXPHOS [22 59 Cil core I IM Tyr Human sperm OXPHOS [8] 60 NAD(P) transhydrogenase IM ? Bovine H* pump [45] 61 ANT IM ? Bovine Transport [45 62 Phosphate carrier protein iM 7 Bovine Transport [45] 63 Aldose reductase" ? S/T? Various cell lines Osmoregulation . [51] Abbreviations: AA, amino acid IS, serine;~T, threonine; Y, tyrosine); ANT, adenine nucleotide transporter; Axmito, mitochondrial annexin; s-OX, P-oxidation; CKAD branched chain ketoacid dehiydrogenase: CI-CV. respiratory chain complexes 1-5: CPT. carnitine palmitoyltransferase: CREB. cAMP-responsive element (Cre)-binding protein: CYP, cytochrome P450; D8P, dodecamer-binding protein; EF. elongation factor: GST. glutathione S-transterase; HSP heat shock protein; IM. Inner membrane; IMS. imermembrane space: M. matrix; MnSOO,. manganese super oxide dismutase; mTERF, mitochondrial transcription termination factor; mtGAT. mitochondrial glycerol-3 phosphatase acetyitransferase; mthsp, mitochondrial HSP; rnTBP; mitochondrial telomere-binding protein; NDI(, nucleoside diphosphate kinase: oM. outer'membrane; OXPHOS; oxidative phosphorylation: P site: site of phosphorylation: PDC E1/3, pyruvate dehydrogenase complexE /3 subunit: PDK, pyruvate dehydrogenase kinase; PLA, phospholipase A: ScIRP, subunit c-immunoreactive peptide: SSAT, spermidinefspermine acetyitransferase StAR, staroidogenic acute regulatory protein: TCA. tricartboxyic acid cycle: TRAP-1, tumor-necrosis factor type 1 receptor-associated protein: VOAC. voltage-dependent. anion channel. "Phosphorylation is observed only so.vitre on recombinant protein. 'Protein translocates to mitochondria (i.e. protein is not a resident mitochondrial protein). 5 WO 2009/123597 PCT/US2008/004410 4 The largest kinase and phosphatase families in the human genome, the protein kinases (PKs) and protein tyrosine phosphatases (PTPs), possess more than 500 and more than 100 members, respectively. Together with smaller families of kinases and phosphatases, these signalling molecules comprise nearly three percent of all proteins encoded in the human 5 genome. Similar to the aforementioned phosphoproteins, kinases and phosphatases have been implicated in mitochondrial functions in a surprising number of studies, and so far at least 25 kinases and eight phosphatases have been reported to localize to mitochondria, as seen in FIGURE 2. These kinases and phosphatases are clearly not restricted to one group or family; rather, they represent nearly every known mammalian kinase and phosphatase 10 subgroup, reflecting the range of signalling pathways that are likely to influence the mitochondrion. These signalling molecules include kinases and phosphatases varying in substrate specificity, (e.g., tyrosine kinases, classic PTP subgroups, serine/threonine kinases, and dual-specific PTPs); in catalytic mechanisms (e.g., cysteine-based PTPs, aspartic acid based PTPs, and metal-dependent phosphatases); and in evolutionary conservation (e.g., 15 bacterially-related pyruvate dehydrogenase kinases (PDKs) and phosphatases (PDPs), branched chain ketoacid dehydrogenase kinase (BCKDK) and phosphatase (BCKDP), and many mammalian-specific enzymes). Most of these signalling molecules possess other non-mitochondrial roles in the cell and are primarily found to exist outside mitochondria. The impetus for, or mechanism of, 20 their translocation to mitochondria is poorly understood for most proteins. What is clear, however, is that kinases and phosphatases, like the phosphoproteins listed earlier, are present in all compartments of the mitochondrion, as evident in FIGURE 3, and that their activities impinge on diverse mitochondrial functions. A few signalling molecules, however, seem to localize primarily to mitochondria. In 25 addition to PDKs and PDPs, this group includes the PTEN-induced kinase PINK1, the dual- WO 2009/123597 PCT/US2008/004410 5 specific PTP targeted to the mitochondrion PTPMT1, and the aspartic-acid-based phosphatase/ATPase Tim50. Although the substrates for many of these proteins are currently unknown, it is clear from biological and genetic data that they possess crucial functions in mitochondria. For example, although its submitochondrial localization remains to be 5 determined, PINK1 is targeted to mitochondria by an N-terminal signal sequence. This kinase, which shares high sequence homology with the Ca+ 2 /calmodulin-regulated kinase family, seems to be involved in pro-survival activities. Similarly, PTPMTl was recently identified as the first PTP that is localized primarily inside the mitochondrion and, like PINK1, is targeted to the mitochondrion by an N-terminal signal peptide and is found tightly 10 associated with the matrix face of the inner mitochondrial membrane. PTPMT1 is highly expressed in pancreatic B cells, whose mitochondria have the important function of coupling glucose metabolism to the secretion of insulin. Finally, Tim50, a key component of the TIM (translocase of the inner membrane) complex, has sequence homology to the CTD family of aspartic-acid-based phosphatases/ATPases. Tim50, like other members of this family, might 15 function as an ATPase, but it has been also shown to possess phosphatase activity against the phosphotyrosine analog para-nitrophenyl phosphate in vitro. Given the above, it can be seen that not only are kinases and phosphatases recruited to mitochondria from elsewhere in the cell, but the mitochondrion itself seems to possess a contingent of resident signalling molecules. 20 Although the effect of phosphorylation on most known mitochondrial phosphoproteins is unclear, with the kinases and phosphatases responsible sometimes remaining unidentified, a few phosphorylation events have been partially characterized. These examples, like the phosphoproteins and signalling molecules discussed earlier, are not restricted to one area of the mitochondrion.

WO 2009/123597 PCT/US2008/004410 6 Phosphorylation on the mitochondrial outer membrane has a crucial role in regulating apoptosis. A particularly well-defined event is the phosphorylation of BAD, a proapoptotic member of the BCL-2 family. It has been shown that PKA, after treatment with the pro survival cytokine interleukin-3, translocates to the outer membrane. Once anchored to an A 5 kinase anchoring protein (AKAP) on the outer membrane, PKA phosphorylates BAD on Ser 112, contributing to the inactivation and disassociation of BAD from mitochondria, a process depicted in FIGURE 3A. Phosphorylation of BAD on Ser 136 by p70S6 kinase and on Ser 155 by in unidentified kinase has also been implicated in the inactivation of BAD. The most well-established example of reversible phosphorylation acting as a 10 regulatory mechanism in healthy cell mitochondria is that of the PDH complex in the matrix, a simplified cartoon of which is illustrated in FIGURE 3B. This complex catalyzes the conversion of glycolysis-derived pyruvate to acetyl-coenzyme A (CoA), the main precursor to the tricarboxylic acid (TCA) cycle. As the link between these two major energy-producing pathways, the PDH complex must be properly regulated for the maintenance of cellular 15 glucose homeostasis. Since its identification as the first mitochondrial phosphoprotein, the PDH complex and its regulation by reversible phosphorylation have been studied exhaustively. Phosphorylation and dephosphorylation of the PDH complex are carried out by PDKs and PDPs, respectively. At least four PDK isoforms and two PDP isoforms are known, all of 20 which are associated with the E2 subunit of the PDH complex. The phosphorylation events occur on three separate serine residues of the El subunit, each leading to significant inactivation of this complex. Notably, there is now at least one report of a PDK itself being phosphorylated. This phosphorylation, carried out by PKC, has been shown to inactivate PDK, potentially demonstrating an additional level of PDH complex regulation by reversible WO 2009/123597 PCT/US2008/004410 7 phosphorylation. Thus, the PDH complex is a prime example of mitochondria using phosphorylation to add a level of regulation to an otherwise conserved process. As indicated by the mitochondrial tyrosine kinases and phosphatases listed earlier, phosphorylation within this organelle is not limited to serine and threonine residues. An 5 example of tyrosine phosphorylation that affects mitochondrial energetics is seen in the regulation of cytochrome c oxidase (COX) in the inner membrane, depicted in FIGURE 3C. COX, as the terminal enzyme in the respiratory chain, coordinately reduces oxygen to water while pumping protons across the inner membrane. Similar to the PDH complex, COX is allosterically regulated by ATP and ADP, as well as the thyroid hormone T 2 and possibly 10 Ca+ 2 ions. In addition to these forms of regulation, it has been shown that COX becomes phosphorylated in a cAMP-dependent manner both in vitro and in HepG2 cells in vivo. COX comprises thirteen subunits and has been crystallized as a dimer. The phosphorylation site has been identified as Tyr 304 of subunit 1, which is located at the dimer interface on the intermembrane. The phosphorylation event markedly inhibits COX activity, perhaps by 15 disrupting dimer formation. In a second example of tyrosine phosphorylation of COX, a portion of the non receptor tyrosine kinase c-Src, similar to the Lyn tyrosine kinase localizes inside mitochondria and leads to tyrosine phosphorylation of COX on an unidentified site of subunit II in osteoclasts. The result of the phosphorylation event is opposite to that seen for subunit I, 20 leading to enhanced COX activity. An important aspect of mitochondrial signalling is how kinases and phosphatases are themselves regulated. Numerous kinases that primarily reside elsewhere in the cell but become targeted to the mitochondrion, such as Abl, Akt, GSK3I3 and PKC6, seem to do so only in their active state. Thus, the extent of some kinase activities within mitochondria 25 might simply be dictated by the number of enzymes that are imported into the organelle.

WO 2009/123597 PCT/US2008/004410 8 For resident signalling molecules, however, different regulatory means must be in place. Although these processes remain to be determined, it is likely that second messengers will have a key role. The activities of the PDK and PDP isoforms are known to be controlled by ions and small molecules such as Mg2+, Ca 2+, K+ and ADP. The characterization of 5 mitochondrial nitric oxide synthases and the recent discovery of a soluble adenylate cyclase in mitochondria provide further opportunities for second messengers to contribute to regulating mitochondrial signalling molecules. Finally, ROS, which have been established as a means of regulating signalling molecules elsewhere in the cell, will almost certainly be involved in regulating kinases and phosphatases in mitochondria, where the bulk of reactive 10 oxygen species is produced. Relative expression levels of isoforms of kinase and phosphatase may play an important role in pathology and linked to other signal transduction events associated with disease. Changes at the gene and expression level may also correlate with such changes. Even after several thorough proteomic surveys, it is estimated that only two-thirds of 15 the mammalian mitochondrial proteome is known. Much of the remaining third is likely to be comprised of low-abundance proteins, such as signalling proteins, which were below the detection level of these mass spectrometric analyses. What is also clear from these studies is the high variability in protein content among mitochondria from different tissues. For example, it has been found that only -50% of the proteins in their proteomics effort were 20 conserved across the four tissues examined (i.e., brain, heart, liver and skeletal muscle). It is likely that different mitochondrial signalling pathways not only will vary from tissue to tissue in the same way but might very well contribute to this observed mitochondrial diversity. Nonetheless, there is more than sufficient evidence to conclude that reversible phosphorylation is involved in the regulation of mitochondrial processes. With over 60 25 reported phosphoproteins, 30 kinases and phosphatases, and various auxiliary signalling WO 2009/123597 PCT/US2008/004410 9 proteins, the mitochondrion is certainly an underappreciated site for signalling by reversible phosphorylation, and in fact such regulation may be useful for the treatment of hyperproliferative diseases such as cancer. The vast majority of fast-growth tumor cells exhibits profound genetic, biochemical, 5 and histological differences with respect to nontransformed cells. Many of these are associated with altered energy metabolism in comparison to the tissue of origin. The most notorious and well-known energy metabolism alteration in tumor cells is an increased glycolytic capacity even in the presence of a high 02 concentration, a phenomenon known as the Warburg effect. 10 Warburg originally proposed that the driving force of the enhanced glycolysis in tumor cells was the energy deficiency caused by an irreversible damage of the mitochondrial function in which, similarly to anaerobic muscle, glucose is converted through glycolysis to lactate, which is later secreted. It has been proposed that this increase in the glycolytic flux in tumor cells is a metabolic strategy to ensure survival and growth in environments with low 15 02 concentrations, such as the partial hypoxia observed in poorly-oxygenated solid tumors. In particular, since the concentration of 02 is lower than 20 pM in many human hypoxic tumors, oxidative phosphorylation is limited therein. Consequently, glycolysis seems to be the main energy pathway in solid tumors (e.g., slow-growing melanomas and mammary adenocarcinoma). 20 A proportional relationship between the rate of cellular proliferation and the rate of ATP supply has been established for fast-growth tumor cells. Some authors have proposed that the glycolytic activity correlates with the degree of tumor malignancy, so that the glycolytic rate is greater in highly de-differentiated and fast-growing tumors than in slower growing tumors or normal cells. In fact, a high level of lactate has been proposed as a 25 predictor of malignancy. That these events are linked to additional signal transduction events WO 2009/123597 PCT/US2008/004410 10 and genetic changes is likely and examples include hypoxic inducing factor and the production and release of angiogenic factors. As depicted in FIGURE 4, for years, the tricarboxylic acid (TCA) cycle was regarded as only being biologically significant only for its role in the production of ATP as an energy 5 source for the organism. However, recent studies have shown that TCA cycle activity also affects signal transduction pathway functions, including cell growth and apoptosis decisions, and that the pertinent glycolytic and TCA cycle enzymes are able to be upregulated or down regulated. There is also a direct correlation between tumor progression and the activities of the glycolytic enzymes hexokinase and phosphofructokinase (PFK) 1, which are greatly 10 increased in fast-growth tumor cells. Accordingly, it has been postulated that tumor cells which exhibit deficiencies in their oxidative capacity are more malignant than those that have an active oxidative phosphorylation. No matter whether under hypoxic or aerobic conditions, then, cancer tissue's reliance on glycolysis is associated with increased malignancy. The role of lipoic acid in the PDH complex of healthy cells has been well studied. 15 The PDH complex has three central subunits, El, E2, and E3 (pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoamide dehydrogenase, respectively). These complexes have a central E2 core, with the other subunits surrounding this core to form the complex. In the gap between these two subunits, the lipoyl domain ferries intermediates between the active sites. The lipoyl domain itself is attached by a flexible linker to the E2 20 core. Upon formation of a hemithioacetal by the reaction of pyruvate and thiamine pyrophosphate, this anion attacks the S1 of an oxidized lipoate species that is attached to a lysine residue. Consequently, the lipoate S2 is displaced as a sulfide or sulfhydryl moiety, and subsequent collapse of the tetrahedral hemithioacetal ejects thiazole, releasing the TPP cofactor and generating a thioacetate on the S 1 of the lipoate. At this point, the lipoate 25 thioester functionality is translocated into the E2 active site, where a transacylation reaction WO 2009/123597 PCT/US2008/004410 11 transfers the acetyl from the "swinging arm" of lipoate to the thiol of coenzyme A. This produces acetyl-CoA, which is released from the enzyme complex and subsequently enters the TCA cycle. The dihydrolipoate, still bound to a lysine residue of the complex, then migrates to the E3 active site, where it undergoes a flavin-mediated oxidation back to its 5 lipoate resting state, producing FADH 2 (and ultimately NADH) and regenerating the lipoate back into a competent acyl acceptor. Should this lipoate species be interrupted, then, there would be no flow of electrons to FADH 2 or generation of acetyl-CoA, and, as a consequence, a toxic buildup of pyruvate within the cell. In cancer cells the production of acetoin has been suggested to be a requirement for cellular detoxification and survival. 10 As stated previously, the activity of the PDH complex in mitochondria is highly regulated by a variety of allosteric effectors and by covalent modification. PDH activity is regulated by its state of phosphorylation, being most active in the dephosphorylated state. PDH phosphorylation is catalyzed by PDK. PDK activity is enhanced by an increase in the level of ATP, NADH, and acetyl-CoA. Negative effectors of PDK are ADP, NAD*, CoA 15 SH, and pyruvate, the levels of which increase when ATP levels fall. While the regulation of PDP, the enzyme which activates PDH through dephosphorylation, is not completely understood, it is known that Mg+ 2 and Ca+2 activate PDP. Two products of the complex, NADH and acetyl-CoA, are negative allosteric effectors of PDH-a, the dephosphorylated active form of PDH. These effectors reduce the 20 affinity of the enzyme for pyruvate, thus limiting the flow of carbon through the PDH complex. In addition, NADH and acetyl-CoA are powerful positive effectors of PDK, the enzyme that inactivates PDH by converting it to the phosphorylated PDH-b form. Since NADH and acetyl-CoA accumulate when the cell energy charge is high, it is not surprising that high ATP levels also up-regulate PDK activity, reinforcing down-regulation of PDH 25 activity in energy-rich cells. However, since pyruvate is a potent negative effector of PDK, WO 2009/123597 PCT/US2008/004410 12 when pyruvate levels rise, PDH-a will be favored even with high levels of NADH and acetyl CoA. Concentrations of pyruvate which maintain PDH-a are sufficiently high so that, in ATP-rich cells, the allosterically down-regulated, high Km form of PDH is nonetheless 5 capable of converting pyruvate to acetyl-CoA. With large amounts of pyruvate in cells having high ATP and NADH levels, pyruvate carbon will be directed to the two main storage forms of carbon (glycogen via gluconeogenesis and fat production via fatty acid synthesis) where acetyl-CoA is the principal carbon donor. Although the regulation of PDP-b is not well understood, it is quite likely regulated to maximize pyruvate oxidation under diminished 10 ATP concentrations and to minimize PDH activity under high ATP concentrations. Tumor cells cannot indefinitely build up pyruvate and associated aldehydes and radicals, such as acetaldehyde, superoxide, hydrogen peroxide, and hydroxyl radicals, as these molecules are cytotoxic at high levels through such mechanisms as drastically lowering cellular pH. It has thus been described, for AS-30D and Ehrlich hepatomas, that a significant 15 fraction of mitochondrial pyruvate is decarboxylated to an active acetaldehyde by the El component of the PDH complex via bound p-hydroxyethylthiamine pyrophosphate. This active acetaldehyde is in turn condensed with a second acetaldehyde, ultimately deacidifying or reducing the original pyruvate, by using either the amino acid glutamine or lipoic acid, to generate acetoin (3-hydroxybutanone), a compound which both competitively inhibits PDH 20 and which is less toxic to the cell than its pyruvate precursor (e.g., by maintaining pH homeostasis within the cell). Despite the importance of acetoin in the pathway of tumor cell detoxification as a result of pyruvate buildup due to the tumor cell's reliance of glycolysis as a source of ATP production, however, there is little reference in the prior art to the effects of blocking the production of acetoin on tumor cell viability.

WO 2009/123597 PCT/US2008/004410 13 Recent studies suggest that forcing cancer cells into more aerobic metabolism suppresses tumor growth. The transition to Warburg metabolism therefore requires shutting down the PDH complex. In this transition, there is enhanced signalling by hypoxia-inducing factor (HIF) in cancer cells, not surprising given HIF's significant role in the metabolism of 5 glucose, as shown in FIGURE 5. Mutations that directly or indirectly instigate HIF signalling in fact appear to be a common mechanism in the development of cancer. HIF induces the overexpression of PDKl, which then acts to lower PDH complex activity. Phosphorylation by PDK1 can be particularly effective for maintaining an inactive PDH complex since this isoform uniquely phosphorylates three serine residues in the alpha subunit of El, the first 10 subunit of the PDH complex. Reactivation of El requires the removal of all three phosphate groups. Furthermore, PDH complex activation may lead to the enhanced ROS production, which may in turn lead to apoptosis. However, alterations in PDKl observed in cancer may not only be due to changes in its concentration but also to changes in its activity and possibly in its amino acid sequence, even between one tumor type or one patient to another. 15 Additionally, PDK1 may form different complexes with various molecules associated with tumors depending upon tumor type. Thus, inhibition of PDK may be a potential target in generating apoptosis in tumors. However, to date, known PDKl inhibitors have been demonstrated to cause maximally only 60% inhibition of this isozyme. While traditional chemotherapy targets dividing, proliferating cells, all clinically 20 accepted chemotherapeutic treatments use large drug doses that also induce profound damage to normal, proliferative host cells. Therefore, more selective targeting is required for the treatment of cancer. Another problem associated with chemotherapy is that, in many tumor types, there is either inherent or acquired resistance to antineoplastic drugs. Overall, traditional chemotherapy currently offers little long-term benefit for most malignant tumors 25 and is often associated with adverse side-effects that diminish the length or quality of life.

WO 2009/123597 PCT/US2008/004410 14 Hence, radical new approaches are required that can provide long-term management of tumors while permitting a decent quality of life. Certainly, drug efficacy, delivery, and side-effects are problems that need to be solved in developing new chemotherapies. In solid tumors, delivery to a hypoxic region may be 5 difficult when the drug does not permeate through the different cellular layers easily. To eliminate these uncertainties, it seems relevant to design anticancer agents having metabolic inhibition constants in, at least, the submicromolar range. It may be argued that cancer cells are genetic and phenotypically heterogeneous from line to line. However, all tumor cell lines depend on glycolysis and oxidative phosphorylation for ATP supply. Concentrating on the 10 Warburg effect allows for designing drugs based on the physico- and biochemical energetic differences between tumor and normal cells to facilitate the design of delivery and therapeutic strategies that selectively affect solely tumor metabolism and growth, without affecting healthy host tissue and organ functionality. US Patents 6,331,559 and 6,951,887 to Bingham et al., as well as US Provisional 15 Application No. 60/912,598 by Bingham et al., all herein incorporated by reference, disclose a novel class of lipoic acid derivative therapeutic agents which selectively target and kill both tumor cells and certain other types of diseased cells. These patents further disclose pharmaceutical compositions, and methods of use thereof, comprising an effective amount of such lipoic acid derivatives along with a pharmaceutically acceptable carrier. However, 20 while these patents describe the structures of and general use for these lipoic acid derivatives, there is no indication in either patent that these derivatives are useful in modulating the structure and/or expression level, and/or regulating the activity, of the PDH complex. As it has been demonstrated that the structure and/or activity of the PDH complex is a critical determinant of tumor activity, then, it would be beneficial to provide for a WO 2009/123597 PCT/US2008/004410 15 pharmaceutically-acceptable modulator of the structure and/or activity, or even the expression level, of the PDH complex, and methods of use thereof. Objects of the Invention and Industrial Applicability 5 Consequently, it is an object of the present invention to provide a pharmaceutical composition to be used in the treatment or diagnosis of a disease, condition, or syndrome characterized by cellular hyperproliferation, such as cancer, which exhibits selective activity in tumor cells. It is a further object of the present invention to provide a pharmaceutical composition 10 to be used in the treatment or diagnosis of such an aforementioned disease, condition, or syndrome which causes minimal side effects upon administration. It is a still further object of the present invention to provide a pharmaceutical composition to be used in the treatment or diagnosis of such an aforementioned disease, condition, or syndrome which is easily manufactured at the least possible cost and is capable 15 of being stored for the longest possible period. It is a still further object of the present invention to provide a pharmaceutical composition to be used in the treatment or diagnosis of such an aforementioned disease, condition, or syndrome which modulates mitochondrial energy metabolism, especially via the structure, activity, and/or expression level of the PDH complex in tumor cell mitochondria. 20 Summary of the Invention To achieve the aforementioned aims, the present invention broadly provides a pharmaceutical composition useful for treating, diagnosing, or preventing a disease, condition, or syndrome characterized by an alteration of the regulation or perturbation of the 25 structure, expression, and/or activity of at least one enzyme and/or enzyme complex, or WO 2009/123597 PCT/US2008/004410 16 subunit thereof, such as the PDH complex, including those characterized by cellular hyperproliferation, such as cancer, or symptoms thereof, in warm-blooded animals, including humans, wherein the pharmaceutical composition comprises an effective amount of at least one lipoic acid derivative, including those as described in US Patents 6,331,559 and 5 6,951,887 and US Provisional Application No. 60/912,598, all herein incorporated by reference, and at least one pharmaceutically-acceptable carrier thereof. By inhibiting mitochondrial energy metabolism, the lipoic acid derivatives of the present invention cause both the loss of mitochondrial membrane potential and other mitochondrial consequences in the diseased cell, resulting in the irreversible initiation of cell 10 death. The lipoic acid derivatives of the present invention may also inhibit mitochondrial energy metabolism by the activation of PDKs and/or inhibition of PDPs or by inhibiting the conversion of pyruvate to the less-toxic molecule acetoin through inhibition of the activity of the El subunit of the PDH complex. The inhibition of acetoin synthesis will distort other processes, including redox balance and may also cause the production of toxic by-products, 15 including acetaldehyde, superoxide, hydrogen peroxide, and hydroxyl radical, these by products themselves consequently causing irreversible damage to the mitochondrion of the diseased cell. The pharmaceutical composition of the present invention may modulate the effects of PDK1, PDK2, PDK3, PDK4, and the mutants or isoforms of each thereof. The 20 pharmaceutical compound may also modulate the effects of PDP 1, PDP2 and the isoforms of each thereof. The pharmaceutical composition of the present invention may also modulate the expression level of the phosphorylase, kinase, and dehydrogenase enzyme constituents found in the PDH complex. This modulation may occur at the transcriptional, translational, or post 25 translational stage, including epigenetic silencing of the appropriate genes.

WO 2009/123597 PCT/US2008/004410 17 As a compound derived from a molecule fundamentally associated with the TCA cycle, and by extension glycolysis, the pharmaceutical composition of the present invention demonstrates selective uptake into tumor cells. Furthermore, such selective tumor cell uptake minimizes the side effects the administration of this pharmaceutical composition would have 5 on healthy non-transformed cells and tissue. In one embodiment of the present invention, the lipoic acid derivatives have the general formula (I): R1 R2 S S O 1 1 1 1

H-CH-CH

2

-CH-(CH

2 )x C-OH (I) wherein R, and R 2 are independently selected from the group consisting of hydrogen, 10 alkyl CnH 2 n+ 1 , alkene CnH 2 n, alkenyl CnH 2 n-I, alkyne CnH 2 n- 2 , alkynyl CnH 2 n- 3 , alkyl sulfide

CH

3

(CH

2 )n-S-, disulfide alkyl CH 3 CHr-S-S-, thiocarbamic ester (CH 2 )nC=NH-, and semithioacetal CH 3 CH(OH)-S-, wherein n is 1-10 and t is 0-9; aromatic; acyl defined as

R

3 C(O)-; heteroaryl; imidoyl defined as R 4 C(=NH)-; organometallic aryl; alkyl organometallic aryl; and semiacetal R 5 CH(OH)-S-; 15 wherein R 1 and R 2 as defined above can be unsubstituted or substituted; wherein R 3 is selected from the group consisting of hydrogen, alkenyl, alkynyl, alkylaryl, heteroaryl, alkylheteroaryl and organometallic aryl, any of which can be substituted or unsubstituted; wherein R 4 is selected from the group consisting of hydrogen, alkenyl, alkynyl, aryl, 20 alkylaryl, heteroaryl, and alkylheteroaryl, any of which can be substituted or unsubstituted; wherein R 5 is CC1 3 , CF 3 , or COOH; and wherein x is 0-16; or salts thereof.

WO 2009/123597 PCT/US2008/004410 18 In a second embodiment of the present invention, the lipoic acid derivatives are defined by a second general formula (II): M

H-CH-CH

2

-CH-(CH

2 )x-C-OH (II) wherein M is a covalent bond, -[C(R)(R 2 )]z-, or a metal chelate or other metal 5 complex where the metal is not palladium; wherein R, and R 2 are independently selected from the group consisting of hydrogen, acyl R 3 C(O)-, alkyl CnH 2 n+ 1 , alkenyl defined as CmH 2 m-, alkynyl defined as CmH 2 m- 3 , aryl, heteroaryl, alkyl sulfide CH 3

(CH

2 )n-S-, imidoyl defined as R 3 C(=NH)-, and hemiacetal defined as R4CH(OH)-S-; 10 wherein Ri and R 2 as defined above can be unsubstituted or substituted; wherein R 3 and R 4 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkylaryl, heteroaryl, and heterocyclyl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of CC1 3 , CF 3 or COOH; 15 and wherein x is 0-16, z is 0-5, n is 0-10 and m is 2-10; or salts thereof. In a third embodiment of the present invention, the lipoic acid derivatives have a third general formula (III): R1 R2 I I S S

(CH

2 )x-R 3 (111) 20 wherein Ri and R 2 are independently selected from the group consisting of hydrogen, alkyl CnH 2 n+ 1 , alkene CLH2n, alkenyl CnH 2 n- 1 , alkyne CnH 2 n- 2 , alkynyl CnH2n-3, alkyl sulfide WO 2009/123597 PCT/US2008/004410 19

CH

3

(CH

2 )n-S-, disulfide alkyl CH 3 CHr-S-S-, thiocarbamic ester (CH 2 )nC=NH-, and semithioacetal CH 3 CH(OH)-S-, wherein n is 1-10 and t is 0-9, aromatic, acyl defined as

R

4 C(O)-, heteroaryl, imidoyl defined as R 5 C(=NH)-, organometallic aryl, alkyl organometallic aryl, semiacetal R 6 CH(OH)-S-, amino acids, carbohydrates, nucleic acids, 5 lipids, and multimers and combinations thereof; wherein Ri and R 2 as defined above can be unsubstituted or substituted; wherein R 3 is selected from a group consisting of amino acids, carbohydrates, nucleic acids, lipids, and multimers thereof; wherein R 4 is selected from the group consisting of hydrogen, alkenyl, alkynyl, 10 alkylaryl, heteroaryl, alkylheteroaryl and organometallic aryl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of hydrogen, alkenyl, alkynyl, aryl, alkylaryl, heteroaryl, and alkylheteroaryl, any of which can be substituted or unsubstituted; wherein R 6 is CC1 3 , CF 3 , or COOH; 15 and wherein x is 0-16; or salts thereof. In a fourth embodiment of the present invention, the lipoic acid derivatives are defined by a fourth general formula (IV): S 'MS

(CH

2 )x-R 3 (IV) 20 wherein M is a covalent bond, -[C(R)(R 2 )]z-, or a metal chelate or other metal complex where the metal is not palladium; wherein Ri and R 2 are independently selected from the group consisting of hydrogen, acyl R4C(O)-, alkyl CnH 2 n+ 1 , alkenyl defined as CmH 2 m-i, alkynyl defined as CmH 2 m- 3 , aryl, heteroaryl, alkyl sulfide CH 3

(CH

2 )n-S-, imidoyl defined as R4C(=NH)-, hemiacetal defined WO 2009/123597 PCT/US2008/004410 20 as R 6 CH(OH)-S-, amino acids, carbohydrates, nucleic acids, lipids, and multimers and combinations thereof; wherein R, and R 2 as defined above can be unsubstituted or substituted; wherein R 3 is selected from a group consisting of amino acids, carbohydrates, nucleic 5 acids, lipids, and multimers thereof; wherein R4 and R 5 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkylaryl, heteroaryl, and heterocyclyl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of CC1 3 , CF 3 or COOH; 10 and wherein x is 0-16, z is 0-5, n is 0-10 and m is 2-10; or salts thereof. Furthermore, as any or all of these general structures may be metabolized within the cell or mitochondrion, it is expressly intended that metabolites of the above-referenced structures are within the scope of the present invention. 15 In each of the general formulae, the (R)-isomer of each particular lipoic acid derivative possesses greater physiological activity than does the (S)-isomer. Consequently, the lipoic acid derivative should be present either solely in its (R)-isomer form or in a mixture of the (R)- and (S)-isomers. In a further aspect of the present invention, there is provided a method of diagnosing, 20 treating, or preventing a disease, condition, syndrome, or symptoms thereof, which includes an alteration of the regulation or perturbation of the structure, expression, and/or function of at least one enzyme and/or enzyme complex, or subunit thereof, such as the PDH complex, including those characterized by cellular hyperproliferation, such as cancer, in warm-blooded animals, including humans, wherein the method comprises administering to such an animal 25 an effective amount of the pharmaceutical composition disclosed herein.

WO 2009/123597 PCT/US2008/004410 21 In a still further aspect of the present invention, there is provided a method of diagnosing and predicting benefit in a patient presenting symptoms of a disease, condition, or syndrome, or symptoms thereof, which includes an alteration of the regulation or perturbation of the structure, expression, and/or activity of at least one enzyme and/or enzyme complex, or 5 subunit thereof, such as the PDH complex, including those characterized by cellular hyperproliferation, such as cancer, comprising obtaining a sample of cells from the patient, administering an effective amount of the pharmaceutical composition of the present invention to the cells in vitro, and obtaining the results therefrom. 10 Brief Description of the Figures The following drawings are illustrative of embodiments of the invention and are not intended to limit the scope of the application as encompassed by the entire specification and claims. FIGURE 1 depicts general signal transduction molecules targeted both into and out 15 from mitochondria and the effects thereof. FIGURE 2 shows a list of mitochondrial kinases and phosphatases and the locations within the mitochondrion thereof. FIGURE 3A illustrates the phosphorylation of BAD by PKA in the outer mitochondrial membrane, and the effects of reversible phosphorylation thereupon. 20 FIGURE 3B presents the conversion of pyruvate into acetyl-CoA in the mitochondrial matrix by the action of the PDH complex, and the effects of reversible phosphorylation thereupon. FIGURE 3C shows the action of COX in reducing oxygen to water and pumping protons across the inner mitochondrial membrane, and the effects of reversible 25 phosphorylation thereupon.

WO 2009/123597 PCT/US2008/004410 22 FIGURE 4 illustrates the structures of substrates and products in the glycolytic production of pyruvate, also showing ATP and NADH generation and associated enzymes. FIGURE 5 shows the regulation of glucose metabolism by HIF-1. FIGURE 6A illustrates the difference in energy metabolism between normal tissue 5 and cancer tissue in vivo. FIGURE 6B depicts the differences between the biogenic forms of lipoic acid in the PDH complex and the lipoic acid derivatives forming part of the pharmaceutical composition of the present invention. FIGURE 6C presents the regulation of the PDH complex by lipoyl residue effects on 10 PDK. FIGURE 7 shows the effects of the pharmaceutical composition of the present invention on xenograft tumor growth. FIGURE 8 shows the effect of treatment with the pharmaceutical composition of the present invention on three tumor cell types and a non-transformed cell. 15 FIGURE 9A shows ATP levels in lung cancer cells after treatment with the pharmaceutical composition of the present invention at or above the lethal threshold. FIGURE 9B compares the pharmaceutical composition of the present invention's inhibition of ATP synthesis in pyruvate-containing media versus glucose-containing media. FIGURE 9C compares the pharmaceutical composition of the present invention's 20 inhibition of ATP synthesis in breast cancer cells to that in normal breast cells. FIGURE 9D compares the pharmaceutical composition of the present invention's inhibition of ATP synthesis with that of lipoic acid and an inactive form of the present invention in lung cancer cells.

WO 2009/123597 PCT/US2008/004410 23 FIGURE 10 illustrates the pharmaceutical composition of the present invention's effects on tumor cell mitochondrial levels of the PDH complex and alpha-ketoglutarate (aKDH) dehydrogenase enzymatic activities. FIGURE 1 A shows Western analyses of two-dimensional gels of extracts from lung 5 cancer cells treated or mock-treated with the pharmaceutical composition of the present invention. FIGURE 11 B shows enlargements of paired two-dimensional gel samples treated and mock-treated with the pharmaceutical composition of the present invention. FIGURE 12A depicts the regulatory role of PDKs as modulated by endogenous 10 lipoate covalently bound to the PDH complex E2 subunit. FIGURE 12B depicts a possible mechanism for differential inactivation of tumor cell PDH complex by the pharmaceutical composition of the present invention. FIGURE 13 presents the effects of the pharmaceutical composition of the present invention on mitochondrial membrane potential in H460 lung cancer cells. 15 FIGURE 14 shows Western blot analysis results wherein cell death pathways in diverse tumor cell types by the pharmaceutical composition of the present invention. Detailed Description of the Invention The present invention is generally directed to pharmaceutical compositions for 20 treating, diagnosing, or preventing a disease, condition, or syndrome, or symptoms thereof, which includes an alteration of the regulation or perturbation of the structure, expression, and/or activity of at least one enzyme and/or enzyme complex, or subunit thereof, such as the PDH complex, including those characterized by cellular hyperproliferation, such as cancer, or symptoms thereof, in warm-blooded animals. Such animals include those of the mammalian 25 class, such as humans, horses, cattle, domestic animals including dogs and cats, and the like, WO 2009/123597 PCT/US2008/004410 24 subject to disease and other pathological conditions and syndromes characterized by cellular hyperproliferation, including cancer. The pharmaceutical composition of the present invention comprises an effective amount of at least one lipoic acid derivative, including those described in US Patents 6,331,559 and 6,951,887 and US Provisional Application No. 5 60/912,598, also known as a thioctan, and a pharmaceutically-acceptable carrier or excipient therefor. As a molecule which is not only a derivative of one which is found normally within mitochondria but also one which is instrumental to the increased glycolytic activity of tumor cells as seen in the Warburg effect, the lipoic acid derivatives of the present invention are particularly well-suited for the selective delivery into and effective concentration within the 10 mitochondria of cells and tissues characterized by hyperproliferation, such as tumorous ones, thereby sparing normal cells and tissue from the effects of the composition. The pharmaceutical composition of the present invention may modulate the effects of PDK1, PDK2, PDK3, PDK4, and the isoforms of each thereof via reversible phosphorylation. The pharmaceutical composition may also modulate the effects of PDP1, PDP2, and the 15 isoforms and/or mutants of each thereof also by reversible phosphorylation. Such modulation may occur through either promotion or inhibition of kinase or phosphatase activity. By inhibiting mitochondrial energy metabolism, the lipoic acid derivatives of the present invention cause both the loss of mitochondrial membrane potential and other mitochondrial consequences in the diseased cell, resulting in the irreversible initiation of cell 20 death. The lipoic acid derivatives of the present invention may also inhibit mitochondrial energy metabolism by the activation of PDKs and/or inhibition of PDPs or by inhibiting the conversion of pyruvate to the less-toxic molecule acetoin through inhibition of the activity of the El subunit of the PDH complex. The inhibition of acetoin synthesis will distort other processes, including redox balance and may also cause the production of toxic by-products, 25 including acetaldehyde, superoxide, hydrogen peroxide, and hydroxyl radical, these by- WO 2009/123597 PCT/US2008/004410 25 products themselves consequently causing irreversible damage to the mitochondrion of the diseased cell. In a first embodiment of the present invention, the lipoic acid derivatives are defined by a first general formula (I): Ri R2 S S O 5 H- CH-CH 2 -CH -(CH 2 )x C--OH ( ) wherein x is 0-16. R, and R 2 can be independently: (1) an acyl group R 3 C(O)-, where R 3 is an alkyl, aryl, or organometallic aryl group, linked through a thioester linkage, including but not limited to acetyl and butaryl, with a specific example being bis-acetyl lipoate; 10 (2) an aromatic group linked through a thioester linkage, including but not limited to benzoyl or a benzoyl derivative, with a specific example being bis-benzoyl lipoate; (3) an alkyl group CnH 2 n+ 1 , where n is 1-10, linked through a thioether linkage with such alkyl groups substituted with other moieties such as, for example, -OH, -Cl or -NH 2 , including but not limited to methyl, ethyl, butyl, decanyl, and 6,8-bis carbomoyl 15 methylipoate; (4) an alkenyl group CnH 2 n- 1 , where n is 2-10, linked through a thioether linkage, including but not limited to propylene, 2,3 dimethyl-2-butene, and heptene; (5) an alkynyl group CnH 2 n- 2 , where n is 2-10, linked through a thioether linkage, including but not limited to acetylene, propyne, and octyne; 20 (6) alkyl, alkenyl, and alkynyl groups which can be either open chains or alicyclics, with the alicyclic groups having additions or substitutions of any of the carbons to form heterocyclics, including but not limited to cyclopropane, cyclopentene, and 6,8 methyl succinimido lipoate; WO 2009/123597 PCT/US2008/004410 26 (7) alkyl, alkenyl, and alkynyl groups which can have additions on any of their carbons, including but not limited to hydroxyls and amines; (8) an aromatic or aryl group linked through a thioether linkage which can be a benzene or a benzene derivative, including but not limited to toluene and aniline; 5 (9) alkyl sulfide groups CH 3

(CH

2 )n-S-, where n can be but is not limited to 0-9, linked through a disulfide linkage; (10) imidoyl groups CHR4C(=NH)-, where n can be but is not limited to 1-10, linked through a thioamide linkage; and (11) semiacetal groups R 5 CH(OH)-S-, where R 5 is limited to compounds with 10 strongly electron withdrawing substituents, including but not limited to trichloroacetaldehyde and pyruvic acid; or salts thereof. R, and R 2 as defined above can be unsubstituted or substituted and may also comprise thioesters that can be oxidized to produce sulfoxides or sulfones, for example, C-S(O)-R and 15 C-S(O) 2 -R, respectively. RI and R 2 may further comprise disulfides that can be oxidized to thiosulfinic or thiosulfonic acids, for example C-S(O)-S-R and C-S(O) 2 -S-R, respectively.

R

3 is selected from the group consisting of hydrogen, alkenyl, alkynyl, alkylaryl, heteroaryl, alkylheteroaryl and organometallic aryl, any of which can be substituted or 20 unsubstituted. Similarly, R 4 is selected from the group consisting of hydrogen, alkenyl, alkynyl, aryl, alkylaryl, heteroaryl, and alkylheteroaryl, any of which can be substituted or unsubstituted.

R

5 is -CC1 3 , -CF 3 , or -COOH. In a second embodiment of the present invention, the lipoic acid derivatives are 25 defined by a second general formula (II): WO 2009/123597 PCT/US2008/004410 27 M H-CH2-C H-(CH2)x-C-OH wherein M is a covalent bond, -[C(Ri)(R 2 )]z-, or a metal chelate or other metal complex where the metal is not palladium; wherein R, and R 2 are independently selected from the group consisting of hydrogen, 5 acyl R 3 C(O)-, alkyl CnH 2 n+ 1 , alkenyl defined as CnH 2 n-, alkynyl defined as CnH 2 n- 3 , aryl, heteroaryl, alkyl sulfide CH 3

(CH

2 )n-S-, imidoyl defined as R 3 C(=NH)-, and hemiacetal defined as R 4 CH(OH)-S-; wherein R, and R 2 as defined above can be unsubstituted or substituted; wherein R3 and R 4 are independently selected from the group consisting of hydrogen, 10 alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkylaryl, heteroaryl, and heterocyclyl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of -CCl 3 , -CF 3 or -COOH; and wherein x is 0-16, z is 0-5, and n is 0-10; or salts thereof. 15 In a third embodiment of the present invention, the lipoic acid derivatives have a third general formula (III): R1 R2 I I S S

(CH

2

)X-R

3 (11) wherein R, and R 2 are independently selected from the group consisting of hydrogen, alkyl CnH 2 n+ 1 , alkene CnH 2 n, alkenyl CnH 2 n-, alkyne CnH 2 n- 2 , alkynyl CH 2 n- 3 , alkyl sulfide 20 CH 3

(CH

2 )n-S-, disulfide alkyl CH 3 CHr-S-S-, thiocarbamic ester (CH 2 )nC=NH-, and semithioacetal CH 3 CH(OH)-S-, wherein n is 1-10 and t is 0-9, aromatic, acyl defined as WO 2009/123597 PCT/US2008/004410 28 R4C(O)-, heteroaryl, imidoyl defined as R 5 C(=NH)-, organometallic aryl, alkyl organometallic aryl, semiacetal R 6 CH(OH)-S-, amino acids, carbohydrates, nucleic acids, lipids, and multimers and combinations thereof; wherein R, and R 2 as defined above can be unsubstituted or substituted; 5 wherein R 3 is selected from a group consisting of amino acids, carbohydrates, nucleic acids, lipids, and multimers thereof; wherein R 4 is selected from the group consisting of hydrogen, alkenyl, alkynyl, alkylaryl, heteroaryl, alkylheteroaryl and organometallic aryl, any of which can be substituted or unsubstituted; 10 wherein R 5 is selected from the group consisting of hydrogen, alkenyl, alkynyl, aryl, alkylaryl, heteroaryl, and alkylheteroaryl, any of which can be substituted or unsubstituted; wherein R 6 is CCl 3 , CF 3 , or COOH; and wherein x is 0-16; or salts thereof. 15 In a fourth embodiment of the present invention, the lipoic acid derivatives are defined by a fourth general formula (IV): S'MsS (0H 2 X-R 3 (IV) wherein M is a covalent bond, -[C(R)(R 2 )]-, or a metal chelate or other metal complex where the metal is not palladium; 20 wherein R, and R 2 are independently selected from the group consisting of hydrogen, acyl R 4 C(O)-, alkyl CnH 2 n+ 1 , alkenyl defined as CmH 2 m-, alkynyl defined as CmH 2 m- 3 , aryl, heteroaryl, alkyl sulfide CH 3

(CH

2 )n-S-, imidoyl defined as R 4 C(=NH)-, hemiacetal defined as R 6 CH(OH)-S-, amino acids, carbohydrates, nucleic acids, lipids, and multimers and combinations thereof; WO 2009/123597 PCT/US2008/004410 29 wherein R, and R 2 as defined above can be unsubstituted or substituted; wherein R 3 is selected from a group consisting of amino acids, carbohydrates, nucleic acids, lipids, and multimers thereof; wherein R 4 and R 5 are independently selected from the group consisting of hydrogen, 5 alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkylaryl, heteroaryl, and heterocyclyl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of CC1 3 , CF 3 or COOH; and wherein x is 0-16, z is 0-5, n is 0-10 and m is 2-10; or salts thereof. 10 Furthermore, as any or all of these general structures may be metabolized within the cell or mitochondrion, it is expressly intended that metabolites of the above-referenced structures are within the scope of the present invention. It has been observed that, in both the first and second general formulae, the (R) isomer of each particular lipoic acid derivative possesses greater physiological activity than 15 does the (S)-isomer. Hence, while both isomers are contemplated for use in the present invention, in particularly preferred embodiments, it is specifically contemplated that the (R) isomer be preferentially used, or that the (R)-isomer be present in a mixture with the (S) isomer. The pharmaceutical composition of the present invention may also modulate the 20 expression levels of the phosphatase, kinase, and dehydrogenase enzyme constituents found in the PDH complex. This modulation may occur at the transcriptional, translational, or post translational stage, including epigenetic silencing of the appropriate genes. The compositions of the present invention may further include a pharmaceutically acceptable carrier or excipients. Examples of pharmaceutically-acceptable carriers are well 25 known in the art and include those conventionally used in pharmaceutical compositions, such WO 2009/123597 PCT/US2008/004410 30 as, but not limited to, antioxidants, buffers, chelating agents, flavorants, colorants, preservatives, absorption promoters to enhance bioavailability, antimicrobial agents, and combinations thereof. The amount of such additives depends on the properties desired, which can readily be determined by one skilled in the art. 5 The pharmaceutical compositions of the present invention may routinely contain salts, buffering agents, preservatives, and compatible carriers, optionally in combination with other therapeutic ingredients. When used in medicine, the salts should be pharmaceutically acceptable, but non-pharmaceutically-acceptable salts may conveniently be used to prepare pharmaceutically-acceptable salts thereof and are not excluded from the scope of the 10 invention. Such pharmacologically- and pharmaceutically-acceptable salts include, but are not limited to, those prepared from the following acids: hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic, acetic, palicylic, p-toluene sulfonic, tartaric, citric, methane sulfonic, formic, malonic, succinic, naphthalene-2-sulfonic, and benzene sulfonic. Also, pharmaceutically-acceptable salts can be prepared as alkaline metal or alkaline earth salts, 15 such as sodium, potassium or calcium salts of the carboxylic acid group. The present invention additionally provides methods for treating or diagnosing a patient with therapeutic or diagnostic agents by delivering an effective amount of at least one therapeutic or diagnostic agent to cells for implementing the prevention, diagnosis, or treatment of a disease, condition, or syndrome, or symptoms thereof, which includes an 20 alteration of the regulation or perturbation of the structure, expression, and/or activity of the at least one enzyme and/or enzyme complex, or subunit thereof, including those characterized by cellular hyperproliferation. Modulating the PDH complex as an improved treatment of cancer is especially contemplated, including treatment of primary tumors by the control of tumor cell proliferation, angiogenesis, metastatic growth, apoptosis, and treatment of the 25 development of micrometastasis after or concurrent with surgical removal; and radiological WO 2009/123597 PCT/US2008/004410 31 or other chemotherapeutic treatment of a primary tumor. The pharmaceutical composition of the present invention is useful in such cancer types as primary or metastatic melanoma, lymphoma, sarcoma, lung cancer, liver cancer, Hodgkin's and non-Hodgkin's lymphoma, leukemias, uterine cancer, cervical cancer, bladder cancer, kidney cancer, colon cancer, and 5 adenocarcinomas such as breast cancer, prostate cancer, ovarian cancer, and pancreatic cancer. For therapeutic and diagnostic applications, the pharmaceutical composition can be administered directly to a patient when combined with a pharmaceutically-acceptable carrier. This method may be practiced by administering the therapeutic or diagnostic agent alone or 10 in combination with an effective amount of another therapeutic or diagnostic agent, which may be, but is not limited to, a glycolytic inhibitor, a microtubule-interacting agent, a cytostatic agent, a folic acid inhibitor, an alkylating agent, a topoisomerase inhibitor, a tyrosine kinase inhibitor, podophyllotoxin or derivatives thereof, an antitumor antibiotic, a chemotherapeutic agent, an apoptosis-inducing agent, an anti-angiogenic agent, nitrogen 15 mustards, nucleic acid intercalating agents, and combinations thereof. Such therapeutic agents may further include other metabolic inhibition reagents. Many such therapeutic agents are known in the art. The combination treatment method provides for simultaneous, sequential, or separate use in treating such conditions as needed to amplify or ensure patient response to the treatment method. 20 The methods of the present invention may be practiced using any mode of administration that is medically acceptable, and produces effective levels of the active compounds without causing clinically unacceptable adverse effects. Although formulations specifically suited for parenteral administration are preferred, the compositions of the present invention can also be formulated for inhalational, oral, topical, transdermal, nasal, ocular, 25 pulmonary, rectal, transmucosal, intravenous, intramuscular, subcutaneous, intraperitoneal, WO 2009/123597 PCT/US2008/004410 32 intrathoracic, intrapleural, intrauterine, intratumoral, or infusion methodologies or administration, in the form of aerosols, sprays, powders, gels, lotions, creams, suppositories, ointments, and the like. If such a formulation is desired, other additives well-known in the art may be included to impart the desired consistency and other properties to the formulation. 5 Those skilled in the art will recognize that the particular mode of administering the therapeutic or diagnostic agent depends on the particular agent selected; whether the administration is for treatment, diagnosis, or prevention of a disease, condition, syndrome, or symptoms thereof; the severity of the medical disorder being treated or diagnosed; and the dosage required for therapeutic efficacy. For example, a preferred mode of administering an 10 anticancer agent for treatment of leukemia would involve intravenous administration, whereas preferred methods for treating skin cancer could involve topical or intradermal administration. As used herein, "effective amount" refers to the dosage or multiple dosages of the therapeutic or diagnostic agent at which the desired therapeutic or diagnostic effect is 15 achieved. Generally, an effective amount of the therapeutic or diagnostic agent may vary with the activity of the specific agent employed; the metabolic stability and length of action of that agent; the species, age, body weight, general health, dietary status, sex and diet of the subject; the mode and time of administration; rate of excretion; drug combination, if any; and extent of presentation and/or severity of the particular condition being treated. The precise 20 dosage can be determined by an artisan of ordinary skill in the art without undue experimentation, in one or several administrations per day, to yield the desired results, and the dosage may be adjusted by the individual practitioner to achieve a desired therapeutic effect or in the event of any complication. Importantly, when used to treat cancer, the dosage amount of the therapeutic agent used should be sufficient to inhibit or kill tumor cells while 25 leaving normal cells substantially unharmed.

WO 2009/123597 PCT/US2008/004410 33 The therapeutic or diagnostic agent included in the pharmaceutical compositions of the present invention can be prepared in any amount desired up to the maximum amount that can be administered safely to a patient. The amount of the diagnostic agent or therapeutic agent may range from less than 0.01 mg/mL to greater than 1000 mg/mL, preferably about 50 5 mg/mL. Generally, the pharmaceutical composition of the present invention will be delivered in a manner sufficient to administer to the patient an amount effective to modulate the structure and/or activity of the PDH complex. The dosage amount may thus range from about 0.3 mg/m 2 to 2000 mg/m 2 , preferably about 60 mg/m 2 . The dosage amount may be 10 administered in a single dose or in the form of individual divided doses, such as from one to four or more times per day. In the event that the response in a subject is insufficient at a certain dose, even higher doses (or effective higher doses by a different, more localized delivery route) may be employed to the extent of patient tolerance. Multiple doses per day are contemplated to achieve appropriate systemic or targeted levels of the therapeutic or 15 diagnostic agent. In yet another embodiment of the present invention, the lipoic acid derivatives of the present invention may be used as diagnostic and predictive agents in vitro. As stated earlier, depending on the specific tumor cell or cell type in question, different lipoic acid derivatives may be more or less effective at inhibiting distinct tumor classes through the modulation of 20 the PDH complex. Thus, for example, in cases where diagnosis or selection of an appropriate chemotherapeutic strategy may be difficult, testing of a culture of tumor cells in vitro with lipoic acid derivatives known to target specific tumor cell types provides an alternative approach for identifying tumor types and effective treatments. Turning to the figures, FIGURE 6A illustrates one of the many likely differences in 25 energy metabolism in normal tissues and tumor cells in vivo. Tumor cells often rely more WO 2009/123597 PCT/US2008/004410 34 heavily on cytoplasmic glycolysis than mitochondrial energy metabolism for ATP generation than do normal cells under corresponding conditions. Changes in expression and regulation of the PDH complex are apparently part of this tumor-specific adaptation. The decreases in the levels of PDH catalytic components and/or increases in the levels of inhibitory PDKs 5 producing these effects may render tumor cells much more vulnerable to agents attacking the PDH complex than are normal cells. FIGURE 6B depicts the structures of lipoic acid as it catalyzes the normal reactions involved in synthesizing acetyl-CoA from pyruvate in the PDH complex. In vivo lipoic acid is joined through its carboxyl terminus in a non-peptide amide linkage to an epsilon amino 10 group of a lysine in the E2 lipoyl domain active sites. Notice also that the oxidation/reduction/acetylation state of PDH E2-bound lipoate is monitored by the kinases and phosphatases that control PDH activity by controlling the phosphorylation inactivation of the Ela PDH subunit. This figure also depicts the structure of the three representative lipoic acid derivatives which may be used in the present invention. While CPI-613 and CPI-045 15 have high anticancer potency, CPI- 157 has little or no activity in cell culture and is useful as a control in several experiments. FIGURE 6C presents the relationship between PDH complex components, including E2 with its bound lipoates, El, and the regulatory PDK. High levels of acetyl-lipoate or dihydrolipoate (not diagrammed) activate PDKs which, in turn, suppress further flux through 20 the PDH complex by inactivating Ela, the subunit catalyzing the first step in PDH complex catalysis. This process acts as a governor for carbon/energy flow through the PDH complex, and this regulatory process is apparently substantially altered to support the variant energy metabolism of tumor cells, as seen in FIGURE 3A. FIGURE 7 shows the effects of the pharmaceutical composition of the present 25 invention on xenograft tumor growth. Cells were implanted subcutaneously on the dorsal WO 2009/123597 PCT/US2008/004410 35 flank as described in EXAMPLE 2. Mice were then injected with the drug (or vehicle alone; "mock") intraperitoneally starting on days as indicated in the figure. The left panel shows a pancreatic tumor model injected three times weekly with the present invention at 1 mg/kg or the vehicle control. This experiment is representative of two done with BxPC-3 cells and of 5 two done with AsPC-1 cells. The right three panels show an H460 lung tumor model injected with the concentrations indicated either once weekly (circles), three times weekly (inverted triangles), or five times weekly (triangles for vehicle treatment and squares for drug treatment). This experiment is representative of four done with H460 cells. FIGURE 8 shows the effect of treatment with the pharmaceutical composition of the 10 present invention on three tumor cell types and a non-transformed cell type (MDCK) either at 200-300 pM ("Treated") or mock treatment ("Mock treated"). Cells were treated in appropriate tissue culture media containing 10% serum or 48 hours. Extensive cell death by apoptosis or apoptosis-like pathways (see also FIGURE 11) in the three cancer cell lines is observed through the methodology described in EXAMPLE 2. In contrast, the non 15 transformed MDCK cells are apparently unaffected by drug treatment at this dose. FIGURE 9A shows ATP levels in H460 lung cancer cells after treatment with the pharmaceutical composition of the present invention at or above the lethal threshold (200pM in 10% serum). Dashed lines represent treatment at the concentrations indicated. Solid lines of corresponding texture represent treatment for the time indicated, followed by removal of 20 the drug and 60 minutes of recovery in the drug-free medium. Block arrows indicated intervals of ATP recovery. FIGURE 9B compares inhibition of ATP synthesis in media in which pyruvate (in the form of methyl-pyruvate) is the primary carbon source (dashed lines) and in which glucose is the primary carbon source (solid lines). Notice that the pharmaceutical composition of the 25 present invention ultimately produces cell death at the same threshold concentrations in both WO 2009/123597 PCT/US2008/004410 36 media; however, early depletion of total cellular ATP levels is high in pyruvate-containing media and absent in glucose-containing media. Also, the onset of cell death is more rapid in the 300pM than the 200pM drug concentration. FIGURE 9C compares the pharmaceutical composition of the present invention's 5 inhibition of ATP synthesis in SK-Br-3 breast cancer cells and HMEC normal breast cells. In contrast to the experiments whose results are depicted in FIGURES 6A and 6B, these experiments were done in serum-free medium (MEBM). As a result, the drug's lethal threshold is lower, approximately 50pM. Note that the small depression in ATP levels in the 22-hour normal cell samples is not related to drug dose and reflects normal experimental 10 variation. FIGURE 9D compares inhibition of ATP synthesis in H460 lung cancer cells by the pharmaceutical composition of the present invention (left graph), lipoic acid (center graph), and an inactive form of the present invention (right graph). As in FIGURE 9C, these experiments are done in serum-free medium so that the drug's lethal threshold is 15 approximately 50gM. FIGURE 10 illustrates the pharmaceutical composition of the present invention's effects (at 400pM in DMEM with 10% serum) on tumor cell mitochondrial levels of PDH (PDC) and (aKDH) enzymatic activities. Notice that PDH is strongly inhibited whereas aKDH is not. Enzyme activity levels are measured in extracts of purified mitochondria using 20 resazurin reduction in response to added carbon source, as described in EXAMPLE 2. The background line corresponds to resazurin reduction in the absence of added carbon source. Next, in FIGURE 11 A, Western analyses of two-dimensional gels of extracts from H460 lung cancer cells treated (+) or mock treated (-) with the pharmaceutical composition of the present invention (at 400 M for 120 minutes in RPMI medium with 10% serum) were 25 performed. The Western transfers were probed with a cocktail of monoclonal antibodies WO 2009/123597 PCT/US2008/004410 37 against Ela and E2 subunits of the PDH complex. The Western transfers are aligned at E2. Notice the substantially higher levels of hyper-phosphorylated and the reduced levels of hypo-phosphorylated forms of El in the drug-treated sample. The left vertical white line illustrates one of the criteria for aligning the gels, the mobility of the E2 subunit. The right 5 vertical white line passes through the less phosphorylated Ela form, the presumptively enzymatically-active component. FIGURE 11 B shows enlargements of paired two-dimensional gel samples treated and mock-treated with the pharmaceutical composition of the present invention. Element A is an enlargement of a portion of FIGURE 8A. Element B is SK-Br-3 breast cancer cells mock 10 treated (-) and treated (+) for 180 minutes with 80pM of the composition in MEBM serum free breast epithelial cell medium. Element C is SK-Br-3 breast cancer cells mock-treated (-) and treated (+) for 240 minutes with 80p.M of the composition in MEBM serum-free breast epithelial cell medium. Element D is HMEC normal breast epithelial cells mock-treated (-) and treated (+) for 240 minutes with 80ptM of the composition in MEBM serum-free breast 15 epithelial cell medium. The vertical white line passes through the less phosphorylated Ela form, the presumptively-enzymatically-active component. FIGURES 12A and 12B depict a working hypothesis for the strong, selective anticancer effects of the pharmaceutical composition of the present invention in vivo. FIGURE 12A, for example, shows the regulatory role of PDKs as modulated by endogenous 20 lipoate covalently bound to the PDC E2 subunit. PDKs normally inactivate the PDC in response to high levels of reduced and/or acetylated lipoate, a process that is apparently substantially modified in tumor cells. Concomitantly, FIGURE 12B shows the large quantitative difference in the ratio of PDK to its substrate PDC-El in the PDC, believed to distinguish normal and tumor cells in 25 vivo. In normal cells the low level of PDK is thought to "walk" hand-over-hand (through its WO 2009/123597 PCT/US2008/004410 38 two dimeric subunits) around the PDH complex, gradually phosphorylating El. This phosphorylation is in steady state equilibrium with PDP dephosphorylation (not diagrammed). On the working hypothesis diagrammed here, thioctans stimulate PDKs through the same sites that normally bind acetyl-lipoate and/or dihydrolipoate, thereby 5 artificially stimulating one or more PDK isoform to inacative Ela. In cancer cells, the much higher levels of PDK might make this stimulation by thioctans much more effective in shutting down PDC enzymatic activity and mitochondrial energy metabolism. The following non-limiting examples are provided to facilitate understanding of the pharmaceutical compositions of the present invention. 10 EXAMPLE 1 CHEMICAL SYNTHESIS OF THIOCTANS Lipoic acid derivatives (i.e., thioctans) CPI-613 and CPI-157 were synthesized by using a modified procedure described in US 6,331,559 BI and US 6,951,887 B2 with 6, 8 15 bismercaptooctanoic acid as the starting material. Thioctan CPI-045 was synthesized as described in US 6,331,559 Bl. Structure analyses for the three thioctans are below. Multiple independent syntheses of CPI-045 and CPI-613 were indistinguishable in their anti-cancer properties. Purity of CPI 613 used in the xenograft (FIGURE 7) and ATP measurements (FIGURE 9) was in excess of 20 99%. All other preparations were greater than 98% pure. CPI-613: 6,8-Bis-benzylsulfanyloctanoic acid: White crystalline solid, m.p. 65-66*C (lit.' 67.5-69*); 'H-NMR (250 MHz, CDCl 3 ): 6 7.15-7.4 (m, 10H), 3.66 (s, 2H), 3.64 (s, 2H), 2.52-2.62 (m, 1H), 2.50 (t, J = 7.6 Hz, 2H), 2.29 (t, J = 7.6 Hz, 2H), 1.2-1.8 (m, 8H); 1 3

C

NMR (62.9 MHz, CDCl3): 5 179.6, 138.6, 138.5, 128.9, 128.8, 128.5, 128.4, 126.9, 44.1, 25 36.4, 35.1, 34.4, 33.8, 28.7, 26.0, 24.4.

WO 2009/123597 PCT/US2008/004410 39 CPI-157: 6,8-Bis-ethylsulfanyloctanoic acid: Colorless oil; TLC (EtAc:Hexanes:HAc, 200:200:1 v/v): Rf = 0.60; 'H-NMR (300 MHz, CDCl3): 8 2.64-2.76 (m, 1H), 2.65 (t, J = 7.5 Hz, 2H), 2.52 (q, J = 7.5 Hz, 2H), 2.49 (q, J = 7.2 Hz, 2H), 2.36 (t, J = 7.4 Hz, 2H), 1.40-1.85 (m, 8H), 1.25 (t, J = 7.2 Hz, 3H), 1.22 (t, J = 7.5 Hz, 3H); "C-NMR 5 (75 MHz, CDCl3): 8 180.0, 44.3, 34.6, 33.9, 28.9, 26.2, 25.9, 24.5, 24.2, 14.9, 14.7; IR (film): 2963, 1708, 1449, 1423, 1283, 1263 cm-1. CPI-045: 6,8-Bis-benzoylsulfanyloctanoic acid: Colorless, viscous oil; TLC (Hexanes:EtAc:HAc, 100:50:1 v/v): Rf = 0.30; 'H-NMR (250 MHz, CDCl3): 6 7.9-8.1 (m, 4H), 7.38-7.60 (m, 6H), 3.8-4.0 (m, 1H), 3.0-3.3 (m, 2H), 2.34 (t, J = 7.1 Hz, 2H), 1.4-2.2 (m, 10 8H); 3 C-NMR (62.9 MHz, CDCl3): 6 191.7, 191.5, 179.7, 137.0, 136.9, 133.3, 128.5, 127.3, 127.1, 43.6, 35.0, 34.6, 33.8, 26.4, 26.2, 24.3; IR (film): 2973, 1710, 1704, 1667, 1665, 1662, 1448, 1207, 1175, 911, 773, 757, 733, 688, 648 cm 1 EXAMPLE 2 15 METHODS USED TO DETERMINE THIOCTAN ANTI-CANCER EFFECTS Cells: Human tumor cell lines were obtained from ATCC and propagated according to ATCC recommendations. Human Mammary Epithelial Cells (HMEC), Small Airway Epithelial Cells (SAEC), and Normal Human Epidermal Keratinocytes (NHEK) primary cells were obtained from LONZA Walkersville, Inc (Walkersville, MD). Each cell line was 20 maintained and propagated in appropriate media developed by and bought from the supplier according to the supplier's instructions. Experiments reported here used normal cells at passage three to six. Tumor growth inhibition studies: CD1-Nu/Nu female mice were implanted with human BxPC-3 or AsPC-1 pancreatic tumor cells or H460 NSCLC by subcutaneous (SC) 25 injection. Approximately 8-12 days later the mice were injected intraperitoneally (IP) at WO 2009/123597 PCT/US2008/004410 40 doses and schedule as indicated in the figure legend. Drug or vehicle was injected at ca. 2ml per 25gm of body weight. Drug concentration was 1.25mg/ml (ca. 3.1mM) or less. The vehicle/solvent consisted of triethanolamine in water at 25mM or less. The vehicle injected in mock treated animals was always identical to the solvent in which the highest drug dose 5 for that experiment was injected. Mice were monitored daily for physical condition and mortality. Body weight and tumor volume were assessed daily before treatment, and approximately three times weekly during and after treatment. Mice were kept on a 12 hour light/dark cycle, were fed ad libitum and were housed at Stony Brook University Animal Facility in accordance with institutional guidelines. 10 Cell death assays: For most assessments of cell viability CellTiter-Glo assay (Promega) was used at times sufficiently long not to be confounded by early thioctan inhibition of ATP synthesis. (FIGURE 9). In a typical experiment, cells were plated in black, clear bottom, 96-well plates at 5,000 cells per well. 18-25 hours later, medium was replaced with fresh medium containing drug solvent (triethanolamine in water at 2.8mM in 15 serum-containing media and 0.7mM in serum-free media) or thioctan CPI-613 in the same solvent. The assay was performed at 24 or 48 hours after drug addition, depending on drug dose, according the manufacturer's directions. In some cases, cells were plated in 48-well plates at 10,000 cells per well, and medium was replaced 18-25 hours later with fresh medium containing drug solvent (,,1% 20 EtOH final concentration) or different concentrations of thioctan CPI-045 in the same solvent. Cells remained in solvent or drug-containing medium for the remainder of the experiment. Plates were inspected at 24, 48 and 72 hours post drug addition, and cell numbers were estimated as a confluence percentage. Under these conditions, thioctan induced cell death is highly apoptotic at near-threshold doses, and cell number estimates are 25 very reliable indicators of death. (FIGURE 10) The integrity of cells remaining at 72 hours, WO 2009/123597 PCT/US2008/004410 41 if any, was tested by trypan blue exclusion. Table 2 provides data regarding the action of thioctans against tumor cells in vitro. Listed are the human tumor and primary human cells we have investigated for sensitivity to CPI-613 and/or CPI-045 killing. "+" indicates that the cells underwent apoptosis or necrosis 5 like cell death at doses of approximately 200-300ptM (in the presence of 10% serum) and approximately 50 pM in serum-free medium. (FIGURES 8 and 9) "--" indicates that these cells required approximately five-fold higher drug doses to induce cell death in the corresponding medium. "nt" indicates non-tested combination. All tumor lines were analyzed in the appropriate media with 10% serum, as were the MDCK normal cells in 10 FIGURE 8. In addition, HMEC, SAEC, NHKC primary human cells, and SK-BR-3, A549 and H460 tumor lines were also analyzed in the appropriate serum-free media. Primary cells were contact inhibited and transformed cells were at comparable densities. ATP assay: Cells were plated in black, clear bottom, 96-well plates at 5,000 cells per well. 18-25 hours later, medium was replaced with fresh medium containing drug solvent 15 (triethanolamine) or thioctan (CPI-613 or CPI-157) or lipoic acid for time interval and at drug concentration as indicated. Cell viability and integrity was assessed by recovery after drug withdrawal by trypan blue exclusion. ATP was measured using CellTiter-Glo luminescence assay (Promega) according to manufacturer's directions. All measurements were performed in duplicate and showed high consistency. The standard error of the mean ranged from 0. 1 20 2% of the measured value. As a result, error bars were omitted from FIGURE 9. Methyl pyruvate medium in FIGURE 9 consisted of RPMI without glucose (Invitrogen), supplemented with 10% dialyzed fetal bovine serum, 5mM HEPES (pH 7.4), and 10mM methylpyruvate (Sigma-Aldrich), and the matched glucose medium was conventional RPMI (Invitrogen). 25 PDH and aKDH enzyme assays: Tumor cells were grown to 80% confluence in 15 WO 2009/123597 PCT/US2008/004410 42 cm plates and treated with CPI-613 as indicated. Mitochondria were isolated according to the method of Moreadith and Fiskum.' Mitochondria were lysed in 0.4% lauryl maltoside. 50pl of mitochondrial lysate was added to 96-well plates. 50 ul of reaction mix (50mM Tris, pH 7.5, 2mM p-NAD+, 225uMv TPP, 2mM pyruvate or a-ketoglutarate, 150IM coenzyme A, 5 2.6mM cysteine, ImM MgCl 2 ) was added to mitochondrial lysates, and the mixture was incubated for 45 minutes at 37"C. At this time, 15ptM resazurin and 0.5U/ml diaphorase were added to the mixture and incubated for an additional five minutes. NADH production was monitored by measuring fluorescence using an excitation wavelength of 530nm and an emission wavelength of 590nm in a microplate reader (Fluorostar). All measurements were 10 performed in duplicate and showed high consistency. The standard error of the mean ranged from 0.3-4% of the measured value. As a result, error bars were omitted from FIGURE 10. El a phosphorylation: Cell lysates for 2-D gels: Cells were grown to 95% confluence in 60 mm dishes and treated with drug or solvent as indicated. Cells were lysed in situ with 450 ptl Lysis buffer A 15 [455ptl Zoom 2D protein solubilizer 1 (Invitrogen), 2.5pl IM Tris base, 5pl lOOX protease inhibitor cocktail (Complete min, EDTA-free, Roche); 5pl 2M DTT]. Cell lysate was transferred to 1.5ml microfuge tubes and sonicated on ice for 15 passes at 50% power. After 10 minute incubation at room temperature, 2.5pl of dimethylacrylamide (DMA, Sigma Aldrich) was added, and lysates were incubated for an additional 10 minutes. 5pjl of 2M 20 DTT were added to neutralize excess DMA. Lysates were centrifuged at 16,000x g for 15 minutes. 2-D gels: We used Zoom Benchtop proteomics system (Invitrogen) according to the manufacturer's direction. Briefly, 30-50pl of lysate were mixed with 0.8pl pH 3-10 ampholytes, 0.

7 5 pl 2M DTT and brought up to 150 pl with Zoom 2D protein solubilizer 1. 25 150 pl of sample was loaded into IPG runner, and pH 3-1ONL IPG strips were added. Strips WO 2009/123597 PCT/US2008/004410 43 were soaked overnight at room temperature. A step protocol was used for isolectric focusing (250V, 20min.; 450V, 15min; 750V, 15 min 2000V, 30min). Strips were treated for 15 minutes in IX loading buffer, followed by 15 minutes in IX loading buffer plus 160mM iodoacetatic acid. Strips were electrophoresed on NuPAGE 4-12% Bis Tris ZOOM gels 5 (Invitrogen).

WO 2009/123597 PCT/US2008/004410 44 Table 2: Effect of thioctans against tumor and primary cells in vitro brain, glioblastoma U-87 MG + + brain, glioblastoma LN-229 + nt 5 breast, adenocarcinoma SK-Br-3 + + breast, adenocarcinoma MCF7 nt + bone, osteosarcoma Saos-2 nt + cervical, adenocarcinoma HeLa + + colorectal, adenocarcinoma SW480 nt + 10 hepatocellular, carcinoma Hep G2 + + Con kidney, carcinoma A-498 + nt lung, carcinoma A459 + + lung, carcinoma H460 + + muscle, rhabdomyosarcoma RD nt + ovarian, carcinoma SKOV-3 + nt 15 pancreatic, adenocarcinoma AsPC-1 + nt pancreatic, adenocarcinoma BxPC-3 + nt prostate, carcinoma LnCaP nt + uterine, sarcoma MesSA + + uterine, sarcoma, MDR Mes-SA/dx5 + + 20 mammary epithelial cells HMEC small airway epithelial cells SAEC -- nt a keratinocytes NHKC nt- WO 2009/123597 PCT/US2008/004410 45 Westerns: Proteins were blotted onto PVDF 4.5pm membranes. PDH Ela and E2 were detected using mAbs (Invitrogen). Caspase-3 and PARP cleavage: Cleaved caspase-3 was detected on Western blots according to Roy and Nicholson.

2 Briefly, after drug or solvent treatment cells were scraped 5 and the medium/cell/apoptotic bodies mixture was centrifuged at 6000x g. Pellet was lysed with lysis buffer C (4M urea, 10% glycerol, 2% SDS, 0.003% BPB; 5% 2-mercaptoethanol). 30 tg of total cell lysate protein per well were loaded on 12% Bis-Tris gels. Proteins blotted onto PVDF 4.5pm membranes. Pro- and active-Caspase-3 were detected with anti-caspase-3 mAb (mouse monocolonal [31A1067]; abcam). PARP cleavage was detected using 10 monoclonal anti-poly (ADP-ribose) polymerase antibody, clone C-2-10 (Sigma-Aldrich). Mitochondrial Ca+ 2 detection: Cells were seeded on 35 mm glass bottom plates (BD Biosciences) at 3x10 5 , grown overnight and treated with drug or solvent as indicated. Cells were then loaded with calcium dye Fluo-4, X-Rhod-1 or Rhod-2 (4 pM, Invitrogen) in phenol red-free media and incubated at 37*C for 10 minutes. Cells were washed once with PBS, and 15 images were captured using an Axiovert 200M, (Zeiss) deconvolution microscope at a fixed exposure time, using FITC filter. Quantification of fluorescence was performed using software provided by the manufacturer. X-Rhod- 1 and Rhod-2 gave similar results (FIGURE 13), indicating that these dyes were measuring a mitochondrial Ca+ 2 signal. References: 20 1. Moreadith RW and Fiskum G. Isolation of Mitochondria from Ascites Tumour-Cells Permeabilized with Digitonin. Analytical Biochemistry 137, 360-367 (1984). 2. Roy S and Nicholson DW. Criteria for identifying authentic caspase substrates during apoptosis. Apoptosis 322,110-125 (2000). 3. Gerencser AA and Adam-Vizi V. Selective, high-resolution fluorescence 25 imaging of mitochondrial Ca2+ concentration. Cell Calcium 30, 311-321 (2001).

WO 2009/123597 PCT/US2008/004410 46 4. Gyorgy H, Gyorgy C, Das S, Garcia-Perez C, Saotome M, Roy SS, and Yi MQ. Mitochondrial calcium signalling and cell death: Approaches for assessing the role of mitochondrial Ca2+ uptake in apoptosis. Cell Calcium 40, 553-560 (2006). 5 EXAMPLE 3 THIOCTANS PERTURB MITOCHONDRIAL MEMBRANE POTENTIAL AND Ca+2 UPTAKE The substrate effects on thioctan inhibition of ATP synthesis (FIGURE 9) indicate that the drug is interfering with the TCA cycle in the mitochondrial matrix. If this is the case, 10 we anticipate that mitochondrial membrane potential' might be compromised at lethal threshold doses and above. Using the potential-sensitive dye TMRE we observe the expected effect. (FIGURE 13) Mitochondrial membrane potential declines rapidly with initiation of drug treatment. The kinetics of membrane potential decline is very similar to the loss of ATP synthesis in the presence of mitochondrial substrates. (FIGURE 9) 15 ATP depletion in mitochondria is known to provoke a homeostatic response that includes the uptake of Ca+ 2 released from cytoplasmic stores, including the endoplasmic reticulum.

2 Moreover, import of this Ca+ 2 into the mitochondrial matrix is thought to require the mitochondrial membrane potential. Thus, we anticipate that thioctan treatment at or above the lethal threshold may produce a sustained cytoplasmic release of Ca+ 2 with transient 20 mitochondrial uptake of the ion in view of progressively compromised membrane potential. Using X-Rhod-1 and Rhod-2 to measure mitochondrial Ca+2 and Fluo-4 to measure cytoplasmic Ca+2 , we observe these expected effects. (FIGURE 13) By around two hours at CPI-doses at and slightly above the lethal threshold (compare FIGURES 9 and 13), as mitochondrial membrane potential declines, this initial mitochondrial 25 Ca+2 transient decays. It is followed at 4-6 hours by a second large mitochondrial Ca+ 2 peak WO 2009/123597 PCT/US2008/004410 47 presumably associated with initiation of the calcium-dependent cell death pathways.

3 References: 1. Garrett R and Grisham CM. Biochemistry. Thomson Brooks/Cole, Southbank, Vic., Australia; Belmont, CA. (2007). 5 2. Graier WF, Frieden M, and Malli R. Mitochondria and Ca2+ signaling: old guests, new functions. Pflugers Archiv-European Journal of Physiology 455, 375-396 (2007). 3. Gyorgy H, Gyorgy C, Das S, Garcia-Perez C, Saotome M, Roy SS, and Yi MQ. Mitochondrial calcium signalling and cell death: Approaches for assessing the role of 10 mitochondrial Ca 2 + uptake in apoptosis. Cell Calcium 40, 553-560 (2006). EXAMPLE 4 THIOCTANS INDUCE DIVERSE CELL DEATH PROGRAMS Reduction in mitochondrial energy metabolism is known to correlate with the 15 decision to enter a cell death pathway in some circumstances, though detailed mechanisms remain incompletely understood.1- 3 At thioctan doses above threshold but within -2-fold of this minimal killing dose, all tested cancer cell types undergo cell death that morphologically resembles apoptosis predominantly. (FIGURE 8) Apoptotic death was confirmed under these conditions by conventional Annexin immunostaning and TUNEL DNA end-labelling 20 assays (results not shown). At higher drug doses (more than ~-2-fold over threshold), active thioctans induce cell death (as assessed by replating viability assays and trypan blue or propidium exclusion) without the morphological correlates of apoptosis, suggesting a necrosis-like pathway (results not shown). 25 These data confirm that the thioctan CPI-613 inhibition mitochondrial energy WO 2009/123597 PCT/US2008/004410 48 metabolism correlates precisely with induction of cell death. The observation that diverse tumor cells, known or presumed to contain inactivating mutations for distinct and diverse cell death pathways 4 are all killed at very similar thioctan doses (FIGURE 8 and Table 2) is striking. This observation suggests that these drugs induce 5 a master signal that is capable of engaging multiple, potentially redundant distal cell death execution pathways.

5 Consistent with this possibility, we find that the Z-VAD-FMK generic caspase inhibitor subtly alters the morphology of cell death in thioctan treated cells, but has no discernible effect on the lethal threshold dose of the drug. 10 To further test the possibility that thioctan-induced cell death can proceed through multiple terminal execution mechanisms we examined caspase-3 and PARP- 1 cleavage, diagnostic of distinct cell death pathways.

5 We find that both thioctans CPI-613 and CPI-045 induce highly variable levels of these two cleavage events in different cells. (FIGURE 14) Collectively, these results indicate that the thioctans are able to induce a strategic 15 commitment to death that, depending on drug dose and cell type, is agnostic about the terminal, tactical execution of that decision. References: 1. Watabe M and Nakaki T. ATP depletion does not account for apoptosis induced by inhibition of mitochondrial electron transport chain in human dopaminergic cells. 20 Neuropharmacology 52, 536-541 (2007). 2. Yuneva M, Zamboni N, Oefner P, Sachidanandam R, and Lazebnik Y. Deficiency in glutamine but not glucose induces MYC-dependent apoptosis in human cells. Journal of Cell Biology 178, 93-105 (2007). 3. Skulachev VP. Bioenergetic aspects of apoptosis, necrosis and mitoptosis. 25 Apoptosis 11, 473-485 (2006).

WO 2009/123597 PCT/US2008/004410 49 4. Johnstone RW, Ruefli AA, and Lowe SW. Apoptosis: A link between cancer genetics and chemotherapy. Cell 108, 153-164 (2002). 5. Cregan SP, Dawson VL, and Slack RS. Role of AIF in caspase-dependent and caspase-independent cell death. Oncogene 23, 2785-2796 (2004). 5 EXAMPLE 5 LIPOIC ACID DERIVATIVE ANALOG STRUCTURES Various non-limiting examples of lipoic acid derivative analogs presented below have been manufactured and are herein disclosed. OH s's s. 10 ry OH 1-01-0 OH s's s, S 6 6 OH 'S S 66a WO 2009/123597 PCT/US2008/004410 50 OH Cs rs OH s. .s SPt The foregoing discussion discloses and describes merely exemplary embodiments of 5 the present invention. One skilled in the art will readily recognize from such discussion, and from the accompanying claims, that various changes, modifications and variations can be made therein without departing from the spirit and scope of the invention as defined in the following claims. Furthermore, while exemplary embodiments have been expressed herein, others practiced in the art may be aware of other designs or uses of the present invention. 10 Thus, while the present invention has been described in connection with exemplary embodiments thereof, it will be understood that many modifications in both design and use will be apparent to those of ordinary skill in the art, and this application is intended to cover any adaptations or variations thereof. It is therefore manifestly intended that this invention be limited only by the claims and the equivalents thereof. 15

Claims (44)

1. A pharmaceutically-acceptable modulator of the regulation or perturbation of the structure, expression, and/or activity of at least one enzyme and/or enzyme complex, or subunit thereof, such as the modified pyruvate dehydrogenase (PDH) complex in the 5 mitochondria of diseased cells of warm-blooded animals, including humans.

2. The modulator of claim 1, wherein the regulation or perturbation comprises reversible phosphorylation or dephosphorylation.

3. The modulator of claim 2, wherein the reversible phosphorylation or dephosphorylation occurs on a kinase, phosphatase, and/or dehydrogenase of an enzyme or 10 enzyme complex, or subunit thereof.

4. The modulator of claim 3, wherein the modulator promotes or inhibits kinase activity.

5. The modulator of claim 4, wherein the kinase is selected from a group comprising pyruvate dehydrogenase kinase (PDK) 1, PDK2, PDK3, PDK4, and isoforms of 15 each thereof.

6. The modulator of claim 3, wherein the modulator promotes or inhibits phosphatase activity.

7. The modulator of claim 6, wherein the phosphatase is selected from a group comprising pyruvate dehydrogenase phosphatase (PDP) 1, PDP2, and isoforms of each 20 thereof.

8. The modulator of claim 3, wherein the modulator promotes or inhibits dehydrogenase activity.

9. The modulator of claim 2, wherein the reversible phosphorylation or dephosphorylation occurs at the PDH complex. 25 10. The modulator of claim 9, wherein the modulation occurs on the Ela subunit WO 2009/123597 PCT/US2008/004410 52 of the PDH complex.

11. The modulator of claim 10, wherein the modulation occurs by inactivation of PDP and the isoforms and mutant forms thereof.

12. The modulator of claim 11, wherein the inactivation of PDP occurs by 5 suppression of PDP expression.

13. The modulator of claim 10, wherein the modulation occurs by activation of PDK and the isoforms and mutant forms thereof.

14. The modulator of claim 1, wherein the diseased cells display sensitivity or insensitivity to treatment with the modulator of claim 1. 10 15. The modulator of claim 14, wherein treatment-insensitive diseased cells may be induced to express at least one modified enzyme or enzyme complex, or subunit thereof, so as to render them treatment-sensitive.

16. The modulator of claim 15, wherein expression is induced by genetic manipulation. 15 17. The modulator of claim 16, wherein the induction is achieved by transcriptional manipulation.

18. The modulator of claim 16, wherein the induction is achieved by translational manipulation.

19. The modulator of claim 16, wherein the induction is achieved by post 20 translational manipulation.

20. The modulator of claim 15, wherein expression is induced by epigenetic manipulation.

21. The modulator of claim 15, wherein expression is induced by phenotypic manipulation. 25 22. The modulator of claim 14, wherein the diseased cells express at least one WO 2009/123597 PCT/US2008/004410 53 modified enzyme or enzyme complex upon treatment with the modulator of claim 1.

23. The modulator of claim 1, wherein the modulator affects the expression level of PDK and the isoforms and mutant forms thereof.

24. The modulator of claim 1, wherein the modulator affects the expression level 5 of PDP and the isoforms and mutant forms thereof.

25. The modulator of claim 23 or 24, wherein the expression level is altered at the level of transcription, translation, or post-translation.

26. The modulator of claim 25, wherein the alteration is epigenetic.

27. The modulator of claim 9, wherein the modulator inhibits the creation of toxic 10 metabolites.

28. The modulator of claim 9, wherein the modulator promotes the detoxification of toxic metabolites.

29. The modulator of claims 27 or 28, wherein the metabolites are selected from a group consisting of acetaldehyde, superoxide, hydrogen peroxide, and hydroxyl radical. 15 30. The modulator of claim 28, wherein the effect of modulation is observed by a decrease in acetoin production.

31. The modulator of claim 9, wherein the reversible phosphorylation or dephosphorylation becomes irreversible.

32. The modulator of claim 31, wherein the effect of the phosphorylation or 20 dephosphorylation results in cell death.

33. The modulator of claim 32, wherein the effect is apoptosis.

34. The modulator of claim 32, wherein the effect is necrosis.

35. The modulator of claim 1, comprising at least one lipoic acid derivative and at least one pharmaceutically-acceptable carrier thereof. 25 36. The modulator of claim 35, wherein the lipoic acid derivative has the formula: WO 2009/123597 PCT/US2008/004410 54 R1 R2 I I S S O H-CH-CH 2 -CH-(CH 2 )x C--OH wherein R, and R 2 are independently selected from the group consisting of hydrogen, alkyl CnH 2 n+ 1 , alkene CnH 2 n, alkenyl CnH 2 n-I, alkyne CnH 2 n- 2 , alkynyl CnH 2 n- 3 , alkyl sulfide CH 3 (CH 2 )n-S-, disulfide alkyl CH 3 CHr-S-S-, thiocarbamic ester (CH 2 )nC=NH-, and 5 semithioacetal CH 3 CH(OH)-S-, wherein n is 1-10 and t is 0-9; aromatic; acyl defined as R 3 C(O)-; heteroaryl; imidoyl defined as R4C(=NH)-; organometallic aryl; alkyl organometallic aryl; and semiacetal R 5 CH(OH)-S-; wherein R, and R 2 as defined above can be unsubstituted or substituted; wherein R 3 is selected from the group consisting of hydrogen, alkenyl, alkynyl, 10 alkylaryl, heteroaryl, alkylheteroaryl and organometallic aryl, any of which can be substituted or unsubstituted; wherein R 4 is selected from the group consisting of hydrogen, alkenyl, alkynyl, aryl, alkylaryl, heteroaryl, and alkylheteroaryl, any of which can be substituted or unsubstituted; wherein R 5 is CCl 3 , CF 3 , or COOH; 15 and wherein x is 0-16; metabolites thereof; or salts thereof.

37. The modulator of claim 35, wherein the lipoic acid derivative has the formula: M H-CH-CH 2 -CH-(CH 2 )x-C-OH 20 wherein M is a covalent bond, -[C(Ri)(R 2 )]z-, or a metal chelate or other metal complex where the metal is not palladium; WO 2009/123597 PCT/US2008/004410 55 wherein R, and R 2 are independently selected from the group consisting of hydrogen, acyl R 3 C(O)-, alkyl CH 2 n+ 1 , alkenyl defined as CH 2 n-I, alkynyl defined as CnH2n.3, aryl, heteroaryl, alkyl sulfide CH 3 (CH 2 )n--S-, imidoyl defined as R 3 C(=NH)-, and hemiacetal defined as R 4 CH(OH)-S-; 5 wherein R, and R 2 as defined above can be unsubstituted or substituted; wherein R 3 and R 4 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkylaryl, heteroaryl, and heterocyclyl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of -CCl 3 , -CF 3 or -COOH; 10 and wherein x is 0-16, z is 0-5, and n is 0-10; metabolites thereof; or salts thereof.

38. The modulator of claim 35, wherein the lipoic acid derivative has the formula: R1 R2 I I S S (CH 2 )x-R 3 15 wherein R, and R 2 are independently selected from the group consisting of hydrogen, alkyl CnH 2 n+ 1 , alkene CnH 2 n, alkenyl CnH 2 n- 1 , alkyne CnH 2 n- 2 , alkynyl CH 2 N- 3 , alkyl sulfide CH 3 (CH 2 )n-S-, disulfide alkyl CH 3 CHt-S-S-, thiocarbamic ester (CH 2 )nC=NH-, and semithioacetal CH 3 CH(OH)-S-, wherein n is 1-10 and t is 0-9, aromatic, acyl defined as R 4 C(O)-, heteroaryl, imidoyl defined as R 5 C(=NH)-, organometallic aryl, alkyl 20 organometallic aryl, semiacetal R 6 CH(OH)-S-, amino acids, carbohydrates, nucleic acids, lipids, and multimers and combinations thereof; wherein R, and R 2 can be unsubstituted or substituted; WO 2009/123597 PCT/US2008/004410 56 wherein R 3 is selected from a group consisting of amino acids, carbohydrates, nucleic acids, lipids, and multimers thereof; wherein R 4 is selected from the group consisting of hydrogen, alkenyl, alkynyl, alkylaryl, heteroaryl, alkylheteroaryl and organometallic aryl, any of which can be substituted 5 or unsubstituted; wherein R 5 is selected from the group consisting of hydrogen, alkenyl, alkynyl, aryl, alkylaryl, heteroaryl, and alkylheteroaryl, any of which can be substituted or unsubstituted; wherein R, is CCl 3 , CF 3 , or COOH; and wherein x is 0-16; 10 metabolites thereof; or salts thereof.

39. The modulator of claim 35, wherein the lipoic acid derivative has the formula: S " S (CH 2 )x- R 3 wherein M is a covalent bond, -[C(R)(R 2 )]z-, or a metal chelate or other metal 15 complex where the metal is not palladium; wherein R, and R 2 are independently selected from the group consisting of hydrogen, acyl R 4 C(O)-, alkyl CnH 2 n+ 1 , alkenyl defined as CmH 2 m-, alkynyl defined as CmH 2 m- 3 , aryl, heteroaryl, alkyl sulfide CH 3 (CH 2 )n-S-, imidoyl defined as R4C(=NH)-, hemiacetal defined as R 6 CH(OH)-S-, amino acids, carbohydrates, nucleic acids, lipids, and multimers and 20 combinations thereof; wherein R, and R 2 can be unsubstituted or substituted; wherein R 3 is selected from a group consisting of amino acids, carbohydrates, nucleic acids, lipids, and multimers thereof; WO 2009/123597 PCT/US2008/004410 57 wherein R 4 and R 5 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkylaryl, heteroaryl, and heterocyclyl, any of which can be substituted or unsubstituted; wherein R 5 is selected from the group consisting of CCl 3 , CF 3 or COOH; 5 and wherein x is 0-16, z is 0-5, n is 0-10 and m is 2-10; metabolites thereof; or salts thereof.

40. The modulator of claims 36, 37, 38, or 39, wherein the lipoic acid derivative is present solely as the (R)-isomer thereof. 10 41. The modulator of claims 36, 37, 38, or 39, wherein the lipoic acid derivative is present as a mixture of the (R)-isomer and the (S)-isomer thereof.

42. The modulator of claim 1, wherein the modulator is useful in the treatment and diagnosis of a disease, condition, or syndrome, or symptoms thereof, which includes an alteration of the structure, expression, and/or activity of at least one enzyme and/or enzyme 15 complex, or subunit thereof.

43. The modulator of claim 42, wherein the at least one enzyme complex is the PDH complex.

44. The modulator of claim 42, wherein the disease, condition, or syndrome is further characterized by cellular hyperproliferation. 20 45. The modulator of claim 44, wherein the disease, condition, or syndrome is cancer.

46. A method of modulating at least one enzyme and/or enzyme complex, or subunit thereof, in a patient presenting a disease, condition, or syndrome which includes an alteration of the structure, expression, and/or activity of the at least one enzyme and/or 25 enzyme complex, or subunit thereof, comprising administration of an effective amount of the WO 2009/123597 PCT/US2008/004410 58 modulator of claim 1.

47. The method of claim 46, wherein at least one enzyme complex is the PDH complex.

48. The method of claim 46, wherein the disease, condition, or syndrome is 5 further characterized by cellular hyperproliferation.

50. The method of claim 48, wherein the disease, condition, or syndrome is cancer.

51. A method of diagnosing and predicting benefit in a patient presenting symptoms of a disease, condition, or syndrome which includes an alteration of the structure, 10 expression, and/or activity of at least one enzyme and/or enzyme complex, or subunit thereof, comprising obtaining a sample of cells from the patient, administering an effective amount of the modulator of claim 1 to the cells in vitro, and obtaining the results therefrom.

52. The method of claim 51, wherein at least one enzyme complex is the PDH complex. 15 53. The method of claim 51, wherein the disease, condition, or syndrome is further characterized by cellular hyperproliferation.

54. The method of claim 53, wherein the disease, condition, or syndrome is cancer.