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Herein, we describe our strategy to design metabolically stable γ-secretase inhibitors which are selective for inhibition of Aβ generation over Notch. We highlight our synthetic strategy to incorporate diversity and chirality. Compounds 30 (ELND006) and 34 (ELND007) both entered human clinical trials. The in vitro and in vivo characteristics for these two compounds are described. A comparison of inhibition of Aβ generation in vivo between 30, 34, Semagacestat 41, Begacestat 42, and Avagacestat 43 in mice is made. 30 lowered Aβ in the CSF of healthy human volunteers.

Proteolytic processing of the amyloid precursor protein (APP) generates amyloid β (Aβ) peptide, which is thought to be causal for the pathology and subsequent cognitive decline in Alzheimer's disease. Cleavage by β-secretase at the amino terminus of the Aβ peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of β-cleaved soluble APP1, and a corresponding cell-associated carboxy-terminal fragment. Cleavage of the C-terminal fragment by γ-secretase(s) leads to the formation of Aβ. The pathogenic mutation K670M671 → N670L671 at the β-secretase cleavage site in APP2, which was discovered in a Swedish family with familial Alzheimer's disease, leads to increased β-secretase cleavage of the mutant substrate3. Here we describe a membrane-bound enzyme activity that cleaves full-length APP at the β-secretase cleavage site, and find it to be the predominant β-cleavage activity in human brain. We have purified this enzyme activity to homogeneity from human brain using a new substrate analogue inhibitor of the enzyme activity, and show that the purified enzyme has all the properties predicted for β-secretase. Cloning and expression of the enzyme reveals that human brain β-secretase is a new membrane-bound aspartic proteinase.

Herein, we describe our strategy to design metabolically stable γ-secretase inhibitors which are selective for inhibition of Aβ generation over Notch. We highlight our synthetic strategy to incorporate diversity and chirality. Compounds 30 (ELND006) and 34 (ELND007) both entered human clinical trials. The in vitro and in vivo characteristics for these two compounds are described. A comparison of inhibition of Aβ generation in vivo between 30, 34, Semagacestat 41, Begacestat 42, and Avagacestat 43 in mice is made. 30 lowered Aβ in the CSF of healthy human volunteers.

Utilizing a pharmacophore hypothesis, previously described gamma-secretase inhibiting HTS hits were evolved into novel tricyclic sulfonamide-pyrazoles, with high in vitro potency, good brain penetration, low metabolic stability, and high clearance.

In this Letter, we report our strategy to design potent and metabolically stable γ-secretase inhibitors that are efficacious in reducing the cortical Aβx-40 levels in FVB mice via a single PO dose.

We have identified the secretory cleavage site in the Alzheimer amyloid precursor (APP) in a non-transfected neuronal cell line, using cyanogen bromide digests of APP purified from medium conditioned by PC-12 cells which were differentiated to a neuronal phenotype. The results obtained are most consistent with proteolysis of the Lys 16 -Leu 17 bond in the β amyloid peptide, followed by partial removal of Lys 16 by a basic carboxypeptidase.

Introduction Inhibition of gamma-secretase presents a direct target for lowering Aβ production in the brain as a therapy for Alzheimer's disease (AD). However, gamma-secretase is known to process multiple substrates in addition to amyloid precursor protein (APP), most notably Notch, which has limited clinical development of inhibitors targeting this enzyme. It has been postulated that APP substrate selective inhibitors of gamma-secretase would be preferable to non-selective inhibitors from a safety perspective for AD therapy. Methods In vitro assays monitoring inhibitor potencies at APP γ-site cleavage (equivalent to Aβ40), and Notch ε-site cleavage, in conjunction with a single cell assay to simultaneously monitor selectivity for inhibition of Aβ production vs. Notch signaling were developed to discover APP selective gamma-secretase inhibitors. In vivo efficacy for acute reduction of brain Aβ was determined in the PDAPP transgene model of AD, as well as in wild-type FVB strain mice. In vivo selectivity was determined following seven days x twice per day (b.i.d.) treatment with 15 mg/kg/dose to 1,000 mg/kg/dose ELN475516, and monitoring brain Aβ reduction vs. Notch signaling endpoints in periphery. Results The APP selective gamma-secretase inhibitors ELN318463 and ELN475516 reported here behave as classic gamma-secretase inhibitors, demonstrate 75- to 120-fold selectivity for inhibiting Aβ production compared with Notch signaling in cells, and displace an active site directed inhibitor at very high concentrations only in the presence of substrate. ELN318463 demonstrated discordant efficacy for reduction of brain Aβ in the PDAPP compared with wild-type FVB, not observed with ELN475516. Improved in vivo safety of ELN475516 was demonstrated in the 7d repeat dose study in wild-type mice, where a 33% reduction of brain Aβ was observed in mice terminated three hours post last dose at the lowest dose of inhibitor tested. No overt in-life or post-mortem indications of systemic toxicity, nor RNA and histological end-points indicative of toxicity attributable to inhibition of Notch signaling were observed at any dose tested. Conclusions The discordant in vivo activity of ELN318463 suggests that the potency of gamma-secretase inhibitors in AD transgenic mice should be corroborated in wild-type mice. The discovery of ELN475516 demonstrates that it is possible to develop APP selective gamma-secretase inhibitors with potential for treatment for AD.

The amyloid beta peptide (A beta P) is a small fragment of the much larger, broadly distributed amyloid precursor protein (APP). Abundant A beta P deposition in the brains of patients with Alzheimer's disease suggests that altered APP processing may represent a key pathogenic event. Direct protein structural analyses showed that constitutive processing in human embryonic kidney 293 cells cleaves APP in the interior of the A beta P, thus preventing A beta P deposition. A deficiency of this processing event may ultimately prove to be the etiological event in Alzheimer's disease that gives rise to senile plaque formation.

Digestion of the native pig kidney fructose 1,6-bisphosphatase tetramer with subtilisin cleaves each of the 35,000-molecular-weight subunits to yield two major fragments: the S-subunit (Mr ca. 29,000), and the S-peptide (Mr 6,500). The following amino acid sequence has been determined for the S peptide: AcThrAspGlnAlaAlaPheAspThrAsnIle Val ThrLeuThrArgPheValMetGluGlnGlyArgLysAla ArgGlyThrGlyGlu MetThrGlnLeuLeuAsnSerLeuCysThrAlaValLys AlaIleSerThrAla z.sbnd;ValArgLysAlaGlyIleAlaHisLeuTyrGlyIleAla. Comparison of this sequence with that of the NH2-terminal 60 residues of the enzyme from rabbit liver (El-Dorry et al., 1977, Arch. Biochem. Biophys.182, 763) reveals strong homology with 52 identical positions and absolute identity in sequence from residues 26 to 60.Although subtilisin cleavage of fructose 1,6-bisphosphatase results in diminished sensitivity of the enzyme to AMP inhibition, we have found no AMP inhibition-related amino acid residues in the sequenced S-peptide. The loss of AMP sensitivity that occurs upon pyridoxal-P modification of the enzyme does not result in the modification of lysyl residues in the S-peptide. Neither photoaffinity labeling of fructose 1,6-bisphosphatase with 8-azido-AMP nor modification of the cysteinyl residue proximal to the AMP allosteric site resulted in the modification of residues located in the NH2-terminal 60-amino acid peptide.

The amino acid sequence has been determined for the insecticyanin from the hemolymph of the fifth instar larvae of the tobacco hornworm, Manduca sexta. The apoprotein is a single polypeptide chain of 189 amino acids, molecular weight 21,378, containing two disulfide bridges, 9-119 and 42-176. The sequence analysis was performed by automated Edman degradation of reduced and carboxymethylated insecticyanin and fragments generated therefrom by cyanogen bromide, trypsin, chymotrypsin, and Staphylococcus aureus proteinase. Most of the peptides were purified by reverse-phase high-performance liquid chromatography. A purification procedure for the isolation of insecticyanin in high yields and a simple method of determining disulfide linkages are also reported.

The interaction of Pseudomanas putida anthranilate synthetase Component II (AS II) with glutamine, glutamine analogs, and iodoacetamide has been investigated in order to clarify the initial steps in the mechanism for glutamine utilization. AS II is alkylated and irreversibly inactivated by covalent attachment of approximately 1 eg of L-2-amino-4-oxo-5-chloropentanoic acid (chloroketone) or 1 eq of iodoacetamide. Alkylation of AS II by chloroketone involves initial formation of an enzyme-inhibitor complex having a Ki of 28 muM. Alkylation of AS II by iodoacetamide occurs without initial formation of a reversible complex. In both cases glutamine protects against alkylation and exhibits competitive kinetics. When anthranilate synthetase Component I (AS I) is associated with AS II, the second substrate, chorismate, enhances alkylation of AS II by chloroketone. Alkylation of AS II by iodoacetamide is unaffected by AS I and chorismate. These results suggest a role of chorismate-AS I complex to promote binding of glutamine to AS II or to facilitate conversion of an AS II-glutamine complex to the covalent glutamyl-AS II intermediate. This conclusion is supported by the fact that glutaminase activity of AS II, which requires formation of the glutamyl-AS II intermediate, is stimulated by AS I and chorismate.

Native pig kidney fructose-1,6-bisphosphatase, in contrast to the rat liver enzyme, is not a substrate of cyclic AMP-dependent protein kinase. However, the pig kidney enzyme becomes a substrate when phosphorylation is performed in 1.6 M urea, after prior unfolding in 8 M urea. A cyanogen bromide fragment containing the phosphorylation site has been isolated and the amino acid sequence of this 63-residue peptide has been determined. This peptide has the following sequence: Leu-Asp-Pro-Ala-Ile-Gly-Glu-Phe-Ile-Leu-Val-Asp-Arg-Asn-Val-Lys-le-Lys-Lys-Lys- Gly-Ser(P)-Ile-Tyr-Ser-Ile-Asn-Glu-Gly-Tyr-Ala-Lys-Glu-Phe-Asp-Pro-Ala-Ile-Thr- Glu-Tyr-Ile-Glu-Arg-Lys-Lys-Phe-Pro-Pro-Asp-Asn-Ser-Ala-Pro-Tyr-Gly-Ala-Arg-Tyr -Val-Gly-Ser-Met. The amino acid sequence around the phosphorylated serine residue resembles those of other protein substrates of cyclic AMP-dependent protein kinase, but it is completely different from the phosphorylation site found in native rat liver fructose-1,6-bisphosphatase.

A procedure is described for purification of the juvenile hormone carrier protein from the last larval instar of Manduca sexta. Homogeneous carrier protein is obtained after three chromatographic steps in up to 36% yield, based upon the recovery from the first gel permeation chromatography step. The sequence of the N- terminus of the polypeptide chain was determined for 19 of the first 20 residues: l 10 Asp-Gln-Gly-Ala-Leu-Phe-Glu-Pro-Cys-Ser- 11 20 Thr-GIn-Asp-lle-Ala-Cys-Leu-Ser- ?-Ala- Three reagents which modify side chain residues in proteins: methyl acetimidate (amino groups), N- succinimidyl -3-(4- hydroxyphenyl ) propionate (amino groups) and tetranitromethane (phenol groups), were reacted with pure carrier protein. In each case, there was relatively little change in the juvenile hormone binding properties of the modified carrier protein.

A hexameric protein of high (18.8%) aromatic amino acid content has been isolated from the haemolymph of pupae of Hyalophora cecropia. It is the major protein present in the haemolymph, and also occurs in the fat body. It is distinct in its behaviour on polyacrylamide gels and in its antigenic reactivity from the two storage proteins of H. cecropia described earlier by Tojo et al. (1978). The new protein is related to similar proteins reported earlier from several species, all of which share the common property of an unusually high content of aromatic amino acid. We propose the generic name arylphorin for such proteins. Hyalophora arylphorin is composed of six seemingly identical subunits of apparent mol.wt. 73,000. Cross-linking studies confirm the hexameric structure, and pore limiting gradient gel electrophoresis of the native protein is consistent with a mol.wt of about 400,000. It contains about 4% carbohydrate, consisting of glucosamine and mannose in a 1:5 molar ratio. The carbohydrate could not be removed by treatment with endoglycosidase H. Hyalophora and Manduca arylphorins are antigenically similar, but their antibodies did not precipitate Calliphora arylphorin. The concentration of Hyalophora arylphorin in haemolymph was examined during the last larval and the pupal-adult moults. In both cases a 95–100% drop in concentration occurred between apolysis and ecdysis.

The complete amino acid sequence of carboxamidomethylated anthranilate synthetase component II (AS II) from Pseudomonas putida has been determined by analysis of cyanogen bromide fragments, tryptic peptides from the citraconylated protein, and by analysis of subdigests of these peptides. AS II is a single polypeptide chain of 197 residues having a calculated molecular weight of 21,684. Previous studies (Goto, Y., Keim, P. S., Zalkin, H., and Heinrikson, R. L. (1976) J. Biol. Chem, 251, 941-949) identified a cysteine residue required for the formation of an acyl-enzyme intermediate. The protein has 3 cysteine residues at positions 54, 79, and 140. Cysteine-79 was alkylated selectively by iodoacetamide and by the glutamine affinity analogue L-2-amino-4-oxo-5-chloropentanoic acid. Based on this evidence cysteine-79 is the active site residue involved in formation of the acyl-enzyme intermediate. Comparison of the P. putida AS II sequence with that of the NH2-terminal 60 residues of the enzyme from Escherichia coli shows 38% sequence identity.

The covalent structure of apolipoprotein A-II, isolated from the serum high-density lipoprotein of a single male Rhesus monkey (Macaca mulatta), was determined. The amino acid sequence of this 77-residue polypeptide is: < Glu-Ala-Glu-Glu-Pro/sup 5/-Ser-Val-Glu-Ser-Leu/sup 10/-Val-Ser-Gln-Tyr-Phe/sup 15/-Gln-Thr-Val-Thr-Asp/sup 20/-Tyr-Gly-Lys-Asp-Leu/sup 25/-Met-G lu-Lys-Val-Lys/sup 30/-Ser-Pro-Glu-Leu-Gln/sup 35/-Ala-Gln-Ala-Lys-Ala/sup 40/-Tyr-Phe-Glu-Lys-Ser/sup 45/-Lys-Glu-Gln-Leu-Thr/sup 50/-Pro-Leu-Val-Lys-Lys/sup 55/-Ala-Gly-Thr-Asp-Leu/sup 60/-Val-Asn-Phe-Leu-Ser/sup 65/-Tyr-Phe-Val-Glu-Leu/sup 70/-Arg-Thr-Gln-Pro-Ala/sup 75/-Thr-Gln-COOH. A comparison of this structure to that of the monomeric form of human apolipoprotein A-II reveals a high degree of homology except for six conservative amino acid replacements (positions 3, 6, 40, 53, 59, and 71). Of particular structural significance is the replacement of cysteine by serine in position 6. This explains why Rhesus A-II exists in monomeric form, contrary to the established dimeric nature of the human protein.

Fructose-1,6-bisphosphatase from rat liver was phosphorylated with cyclic AMP-dependent protein kinase and [gamma-32P]ATP. Brief exposure of the 32P-labeled enzyme to trypsin removed all radioactivity from the enzyme core and produced a single-labeled peptide. The partial sequence of the 17-amino acid peptide was found to be Ser-Arg-Pro-Ser(P)-Leu-Pro-Leu-Pro-(Ser2, Glx2, Pro2, Leu, Arg2). The kinetics of cyclic AMP-dependent protein kinase-catalyzed phosphorylation of native fructose bisphosphatase were compared with those of rat liver type L pyruvate kinase where the sequence around the phosphoserine is known (Arg-Arg-Ala-Ser(P)-Val; Hjelmquist, G., Anderson, J., Edlund, B., and Engstrom, L. (1974) Biochem. Biophys. Res. Commun. 61, 559-563). The Km for pyruvate kinase (17 microM) was less than that for fructose bisphosphatase (58 microM); the Vmax was about 3-fold greater with pyruvate kinase as substrate. The relationship between the rates of phosphorylation of these native substrates and the amino acid sequences surrounding the phosphorylated sites is discussed.

Silkmoth eggshell (chorion) proteins have been characterized by electrophoresis on sodium dodecyl sulfate and isoelectric focusing polyacrylamide gels; up to 33 and 41 components, respectively, were detected from a single chorion. Some of these components are polymorphic, being absent from chorions of certain animals. A system of nomenclature for all chorion proteins is presented, based on their separation on sodium dodecyl sulfate and isoelectric focusing gels. The chorion is enriched in glycine, alanine, cysteine, and tyrosine and poor in methionine and histidine. The proteins were fractionated into four partially overlapping groups; all four are enriched in the above amino acids, although significant differences exist. Further fractionation by isoelectric focusing of one of the above groups, s/s, yielded seven components, two of which are homogeneous both on sodium dodecyl sulfate and isoelectric focusing gels. The amino acid compositions, molecular weights, and solubility properties of the components share certain features which distinguish s/s as a group from the other three groups. The sequence of the first 67 NH2-terminal residues of a homogeneous protein purified from s/s has been determined. The protein contains a cysteine-rich tail (3 cysteines in the first 18 residues) followed by a 49-residue segment which contains only a single cysteine residue. This latter segment also contains two different tetrapeptide sequences which are each repeated, one twice and the other four times.

Human platelet factor 4, a protein that binds heparin, has been purified to apparent homogeneity and the complete amino acid sequence of the protein has been determined. The 70-residue polypeptide chain contains no methionine, tryptophan, or phenylalanine, and contains only a single tyrosyl residue. The sequence analysis demonstrates a highly negatively charged amino-terminal region. The carboxyl-terminal region of the polypeptide is unusual in that it contains a repetitive clustering of positively charged and hydrophobic pairs of amino acids; preliminary evidence suggests that this domain may play a role in the binding of heparin.

Evidence from molecular weight studies and sequence analysis of bovine liver rhodanese indicates that the enzyme is a single polypeptide of molecular weight 35,200, and not a dimer of identical subunits half this size. The rhodanese molecule contains 317 amino acids including 5 methionines, 4 cysteines, and 5 tryptophans. As expected, six fragments were produced by cleavage with cyanogen bromide and these have been aligned in the enzyme with the aid of overlapping tryptic peptides isolated from a [ 14 C] carboxymethylmethionyl rhodanese derivative. The cyanogen bromide fragments account for all of the amino acid residues of the parent rhodanese molecule. Methionine residues are located at positions 72, 112, 214, 217, and 235 in the polypeptide chain and the active site cysteine is at position 251, in the carboxyl-terminal segment of the molecule.

An investigation of the primary structure of the basic chromosomal protein of rat spermatozoa by automated Edman degradation and by carboxypeptidase digestion has provided a general structural outline of the entire molecule. The exact or approximate location of virtually all residues other than arginine or cysteine is reported. Of particular interest, because of the occurrence of phosphorylated derivatives of this protein, is the location of three of the four serine residues.

Automated Edman degradation of reduced and carboxymethylated phospholipase A2-α from Crotalus adamanteus venom revealed a single amino acid sequence extending 30 residues into the protein from the amino terminus. The singularity of the sequence and the yields of the phenylthiohydantoin amino acids thus obtained indicate that the subunits comprising the phospholipase dimer are identical. Further chemical evidence in support of subunit identity was obtained by cleavage of phospholipase A2-α with cyanogen bromide. Compositional analysis of the protein revealed one residue of methionine per monomer and the sequence determination placed this amino acid at position 10 in the sequence of 133 amino acids. Cyanogen bromide cleavage of the protein, followed by reduction and carboxymethylation afforded the expected 2 fragments: an NH2-terminal decapeptide (CNBr-1) and a larger COOH-terminal fragment of 123 residues (CNBr-II). Automated Edman degradation of the latter has extended the sequence analysis to 54 residues in the NH2-terminal segment of the monomer chain. Comparison of this sequence with those derived for phospholipases from other snake venoms, from bee venom, and from porcine pancreas has revealed striking homologies in this region of the molecules. As expected on the basis of their phylogenetic classification, the phospholipases from the pit vipers C. adamanteus and Agkistrodon halys blomhoffii are more similar to one another in sequence than to the enzyme from the more distantly related viper, Bitis gabonica. Furthermore, the very close similarities in sequence observed among all of these phospholipases in regions corresponding to residues 24 through 53 in the C. adamanteus enzyme suggest that this segment of the polypeptide plays an important role in phospholipase function and probably constitutes part of the active site.

Publisher Summary Since the discovery of proinsulin, post-translational modification of proteins by limited intracellular proteolysis has been recognized increasingly as a normal biosynthetic mechanism in the production of a wide variety of secretory, along with some viral, proteins. Little is known about the processing mechanisms involved, aside, in a few instances, from their tentative intracellular localization to the Golgi area, and some elements of their cleavage specificity. This chapter presents several interesting recent examples of pro-proteins and discusses the general significance of these formsMost small polypeptide hormones are derived via cleavage of larger precursor molecules. A number of examples are summarized; however, additional suggestive evidence of the existence of larger forms of somatostatin, pancreatic polypeptide, calcitonin, and vasopressin, as well as others is accumulating. These larger forms may fulfill a number of important functions in biosynthesis and secretion; however, a requirement for a minimum chain length of 65–70 residues for successful vectorial discharge and sequestration in the rough endoplasmic reticulum may provide an explanation for the existence of many of them.

SUMMARY Recent studies have established that limited intracellular proteolysis may participate at several stages in the biosynthesis of many small polypeptide hormones, as exemplified by insulin. Conversion of proinsulin to insulin by trypsin-and carboxypeptidase B-like enzymes occurs in the pancreatic B cell after the peptide has been sequestered from the cytosolic compartment and transported to the Golgi area. An earlier role for proteolysis concerns the conversion of the initial translation product, preproinsulin, to proinsulin during its compartmentalization in the rough endoplasmic reticulum. Preproinsulin, a methionine-initiated peptide which contains a hydrophobic 24-residue NH 2 -terminal extension, was originally identified as the product of the cell-free translation of insulin mRNA, but more recently it has also been detected in small amounts in intact rat islets. Its rapid formation and disappearance during pulse-chase studies are consistent with its role as a biosynthetic precursor and with the proposal that the prepeptide region serves as a leader sequence in the formation of the ribosome-membrane junction and in the vectorial discharge of the peptide. A model for segregation is presented, based on important structural features and physical properties of the prepeptides which may enable these to enter and span the microsomal membrane. Studies on insulin mRNA obtained from transplantable islet cell tumors indicate that the major component contains approximately 600 nucleotides and possesses a 5′ “cap” structure as well as a 3′ polyadenylate “tail”. A closer examination of the insulin tumor mRNA has also revealed two larger polyadenylated RNA fractions having apparent molecular weights of 280,000 and 360,000. These forms, which hybridize to the rat insulin genes and which were shown by ribonuclease T 1 digests to share nucleotide sequences with the major mRNA component, may represent precursors of the mature template. These results indicate that several sequential stages of macromolecular processing are required in the formation of the secreted hormone.

Whole nucleic acid fractions of isolated rat islets of Langerhans greatly stimulate incorporation of radioactive amino acids into protein in a wheat germ ribosomal system. Approximately 30% of the synthetic product is precipitated with antisera to insulin or proinsulin. Characterization of this material by gel chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicates a molecular mass of 11,500 daltons. Trypsin digestion releases intact A chain as well as tryptic fragments of the C-peptides and B chains of the two rat proinsulins. Automated sequence determination of labeled cell-free product purified by immunoprecipitation discloses the presence of 23 additional amino acids NH2-terminal to the B chain sequence of proinsulin. The partial amino acid sequence of this extension is as follows: NH2-X-Leu (Lys) Met-x-Phe-Leu-Phe-Leu-Leu (Lys) Leu-Leu-x-leu-X-X-X-X-X-X-X-X-proinsulin. On the basis of the above evidence we have designated this peptide preproinsulin.

Newly synthesized rat islet proteins have been analyzed by polyacrylamide slab gel electrophoresis and fluorography. A minor component having an apparent molecular weight of 11,100 was identified as preproinsulin by the sensitivity of its synthesis to glucose, the pattern of NH2-terminal leucine residues, and the rapidity of its appearance and disappearance during incubation of islets or islet cell tumors. A small amount of labeled peptide material which may represent the excised NH2-terminal extension of preproinsulin or its fragment was also detected. The kinetics of formation and processing of the preproinsulin fraction were complex, consisting of a rapidly turning over component having a half-life of about 1 min and a slower minor fraction that may have bypassed the normal cleavage process. The electrophoretic resolution of the preproinsulin and proinsulin fractions into two bands each is consistent with the presence of two closely related gene products in rat islets rather than intermediate stages in the processing of these peptides.

A comprehensive, unbiased inventory of synuclein forms present in Lewy bodies from patients with dementia with Lewy bodies was carried out using two-dimensional immunoblot analysis, novel sandwich enzyme-linked immunosorbent assays with modification-specific synuclein antibodies, and mass spectroscopy. The predominant modification of alpha-synuclein in Lewy bodies is a single phosphorylation at Ser-129. In addition, there is a set of characteristic modifications that are present to a lesser extent, including ubiquitination at Lys residues 12, 21, and 23 and specific truncations at Asp-115, Asp-119, Asn-122, Tyr-133, and Asp-135. No other modifications are detectable by tandem mass spectrometry mapping, except for a ubiquitous N-terminal acetylation. Small amounts of Ser-129 phosphorylated and Asp-119-truncated alpha-synuclein are present in the soluble fraction of both normal and disease brains, suggesting that these Lewy body-associated forms are produced during normal metabolism of alpha-synuclein. In contrast, ubiquitination is only detected in Lewy bodies and is primarily present on phosphorylated synuclein; it therefore likely occurs after phosphorylated synuclein has deposited into Lewy bodies. This invariant pattern of specific phosphorylation, truncation, and ubiquitination is also present in the detergent-insoluble fraction of brain from patients with familial Parkinson's disease (synuclein A53T mutation) as well as multiple system atrophy, suggesting a common pathogenic pathway for both genetic and sporadic Lewy body diseases. These observations are most consistent with a model in which preferential accumulation of normally produced Ser-129 phosphorylated alpha-synuclein is the key event responsible for the formation of Lewy bodies in various Lewy body diseases.