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(12) Patent Application Publication (10) Pub. No.: US 2004/0101874 A1 Ghosh Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2004/0101874 A1 Ghosh Et Al US 2004O101874A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2004/0101874 A1 Ghosh et al. (43) Pub. Date: May 27, 2004 (54) TARGETS FOR THERAPEUTIC (22) Filed: Apr. 4, 2003 INTERVENTION IDENTIFIED IN THE MTOCHONDRIAL PROTEOME Related U.S. Application Data (75) Inventors: Soumitra S. Ghosh, San Diego, CA (60) Provisional application No. 60/412,418, filed on Sep. (US); Eoin D. Fahy, San Diego, CA 20, 2002. Provisional application No. 60/389,987, (US); Bing Zhang, Spring, TX (US); filed on Jun. 17, 2002. Provisional application No. Bradford W. Gibson, Berkeley, CA 60/372,843, filed on Apr. 12, 2002. (US); Steven W. Taylor, San Diego, CA (US); Gary M. Glenn, Encinitas, Publication Classification CA (US); Dale E. Warnock, San Diego, CA (US); Sara P. Gaucher, (51) Int. Cl." ........................... C12O 1/68; C12N 1/00 Castro Valley, CA (US) (52) U.S. Cl. ............................................. 435/6; 435/317.1 Correspondence Address: ABSTRACT SEED INTELLECTUAL PROPERTY LAW (57) GROUP PLLC 701 FIFTHAVE Mitochondrial targets for drug Screening assays and for SUTE 6300 therapeutic intervention in the treatment of diseases associ SEATTLE, WA 98104-7092 (US) ated with altered mitochondrial function are provided. Com plete amino acid sequences SEQ ID NOS:1-3025 of (73) Assignees: MitoKor Inc., San Diego, CA (US); The polypeptides that comprise the human heart mitochondrial Buck Institute for Age Research, proteome are provided, using fractionated proteins derived Novato, CA (US) from highly purified mitochondrial preparations, to identify previously unrecognized mitochondrial molecular compo (21) Appl. No.: 10/408,765 nentS. Patent Application Publication May 27, 2004 Sheet 1 of 5 US 2004/0101874 A1 FIGURE (A) - 35000 -o- Complex 5. 30000 - A - Complex V 25000 -v- Complex ill 20000 -o- Complex g 15000 -o- Complex IV is 10000 O w 5000 M (B) Patent Application Publication May 27, 2004 Sheet 2 of 5 US 2004/0101874 A1 FCURE 2 080z WOO3 Patent Application Publication May 27, 2004 Sheet 3 of 5 US 2004/0101874 A1 FIGURE 3 s co El O O O ea 5 CNcy cN t co 2 V se Patent Application Publication May 27, 2004 Sheet 4 of 5 US 2004/0101874 A1 FIGURE 4 998|| AISueulemee Patent Application Publication May 27, 2004 Sheet 5 of 5 US 2004/0101874 A1 FIGURES Eipeps with Trp-ox dipeps with out Metox Eipeps with Metox US 2004/0101874 A1 May 27, 2004 TARGETS FOR THERAPEUTIC INTERVENTION mtDNA encodes 22 tRNAS, two ribosomal RNAS (12s and IDENTIFIED IN THE MITOCHONDRIAL 16S rRNA) and only 13 polypeptides, which are enzymes of PROTEOME the electron transport chain (ETC), the elaborate multi Subunit complex mitochondrial assembly where, for CROSS-REFERENCES TO RELATED example, respiratory oxidative phosphorylation takes place. APPLICATIONS (See, e.g., Wallace et al., in Mitochondria & Free Radicals in Neurodegenerative Diseases, M. F. Beal, N. Howell and 0001) This application claims the benefit of U.S. Provi I. BodisWollner, eds., 1997 Wiley-Liss, Inc., New York, pp. sional Patent Applications No. 60/412,418, filed Sep. 20, 283-307, and references cited therein; see also, e.g., Schef 2002; 60/389,987, filed Jun. 17, 2002; and 60/372,843, filed fler, I. E., Mitochondria, 1999Wiley-Liss, Inc., New York.) Apr. 12, 2002. Mitochondrial DNA thus includes gene Sequences encoding seven subunits of NADH dehydrogenase, also known as STATEMENT REGARDING SEQUENCE ETC Complex I (ND1, ND2, ND3, ND4, ND4L, ND5 and LISTING SUBMITTED ON CD-ROM ND6); one subunit of ETC Complex III (ubiquinol: cyto 0002 The Sequence Listing associated with this applica chrome c oxidoreductase, Cytb); three cytochrome c oxidase tion is provided on CD-ROM in lieu of a paper copy, and is (ETC Complex IV) subunits (COX1, COX2 and COX3); hereby incorporated by reference into the Specification. and two proton-translocating ATP synthase (Complex V) Three CD-ROMs are provided, containing identical copies subunits (ATPase6 and ATPase8). All other mitochondrial of the sequence listing: CD-ROM No. 1 is labeled COPY 1, constituent polypeptides are presumed to be encoded by contains the file 465.app.txt which is 14.4 MB and created genes of the extramitochondrial genome, and the number on Apr. 4, 2003; CD-ROM No.2 is labeled COPY 2, contains and identities of a large number of these polypeptides remain the file 465.app.txt which is 14.4 MB and created on Apr. 4, unknown. Accordingly, for most of the estimated 25,000 2003; CD-ROM No. 3 is labeled CRF, contains the file 40,000 proteins encoded by the human nuclear genome 465.app.txt which is 14.4 MB and created on Apr. 4, 2003. (Venter et al., 2001 Science 291: 1304; Lander et al., 2001 Nature 409:860) little is known regarding subcellular local BACKGROUND OF THE INVENTION ization, for example, which proteins may be molecular components of mitochondria. 0003) 1. Field of the Invention 0008 Mitochondria contain an outer mitochondrial mem 0004. The present invention relates generally to compo brane that Serves as an interface between the organelle and Sitions and methods for identifying mitochondrial proteins the cytosol, a highly folded inner mitochondrial membrane that are useful as targets for therapeutic intervention in that appears to form attachments to the Outer membrane at treating diseases associated with altered mitochondrial func multiple Sites, and an intermembrane Space between the two tion. More Specifically, the invention is directed to pro mitochondrial membranes. The Subcompartment within the teomic profiling of proteins and polypeptides of mitochon inner mitochondrial membrane is commonly referred to as dria and to uses of mitochondrial polypeptides in Screening the mitochondrial matrix (for review, See, e.g., Ernster et al., assays for, and as targets of, therapeutic agents. 1981 J. Cell Biol. 91:227s.) The cristae, originally postu 0005 2. Description of the Related Art lated to occur as infoldings of the inner mitochondrial 0006 Mitochondria are the complex subcellular membrane, have recently been characterized using three organelles that manufacture bioenergetically essential dimensional electron tomography as also including tube-like adenosine triphosphate (ATP) by oxidative phosphorylation, conduits that may form networks, and that can be connected and that promote direct and indirect biochemical regulation to the inner membrane by open, circular (30 nm diameter) of a wide array of cellular respiratory, oxidative and meta junctions (Perkins et al., 1997, JI. of Struct. Biol. 119:260). bolic processes, including aerobic respiration and intracel While the outer membrane is freely permeable to ionic and lular calcium regulation. For example, mitochondria provide non-ionic Solutes having molecular weights less than about the Subcellular site for physiologically important processes ten kilodaltons, the inner mitochondrial membrane exhibits Such as the Krebs cycle, the urea cycle, fatty acid B-Oxida Selective and regulated permeability for many Small mol tion, and heme Synthesis. Mitochondria also participate in ecules, including certain cations, and is impermeable to mechanisms of apoptosis, or programmed cell death (e.g., large (greater than about 10 kD) molecules. Newmeyer et al., Cell 79:353-364, 1994; Liu et al., Cell 0009 Four of the five multisubunit protein complexes 86:147-157, 1996), which is apparently required for, inter (Complexes I, III, IV and V) that mediate ETC activity are alia, normal development of the nervous System and proper localized to the inner mitochondrial membrane. The remain functioning of the immune System. ing ETC complex (Complex II) is situated in the matrix. In at least three distinct chemical reactions known to take place 0007 Functional mitochondria contain gene products within the ETC, protons are moved from the mitochondrial encoded by mitochondrial genes situated in mitochondrial matrix, across the inner membrane, to the intermembrane DNA (mtDNA) and by extramitochondrial (e.g., nuclear) Space. This disequilibrium of charged Species creates an genes not situated in the circular mitochondrial genome. electrochemical membrane potential of approximately 220 While it has been estimated that a functional human mito mV referred to as the “protonmotive force” (PMF). The chondrion contains on the order of 1,000-1,500 distinct PMF, which is often represented by the notation Ap, corre proteins (Lopez et al., 2000 Electrophoresis 21:3427; Schef sponds to the Sum of the electric potential (Alpm) and the pH fler, I. E., Mitochondria, 1999 Wiley-Liss, Inc., New York; differential (ApH) across the inner membrane according to Rabilloud et al., 1998 Electrophoresis 19:1006; Schefflere the equation tal., 2001 Mitochondrion 1:161; Schatz, G., 1995 Biochem. Biophys. Acta Mol. Basis Dis. 1271:123), the 16.5 kb Ap=AGom-ZApH US 2004/0101874 A1 May 27, 2004 0010 wherein Z stands for -2.303 RT/F. The value of Z 0013 For instance, free radical production in biological is -59 at 25 C. when Ap and Alpm are expressed in mV and Systems is known to result in the generation of reactive ApH is expressed in pH units (See, e.g., Ernster et al., J. Cell Species that can chemically modify molecular components Biol. 91:227s, 1981 and references cited therein). of cells and tissues. Such modifications can alter or disrupt Structural and/or functional properties of these molecules, 0.011 Aum provides the energy for phosphorylation of leading to compromised cellular activity and tissue damage. adenosine diphosphate (ADP) to yield ATP by ETC Com Mitochondria are a primary Source of free radicals in bio pleX V, a process that is coupled Stoichiometrically with logical Systems (see, e.g., Murphy et al., 1998 in Mitochon transport of a proton into the matrix. Alm is also the driving dria and Free Radicals in Neurodegenerative Diseases, force for the influx of cytosolic Ca" into the mitochondrion. Beal, Howell and Bodis-Woliner, Eds., Wiley-Liss, New Under normal metabolic conditions, the inner membrane is York, pp.
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