Phe*-Ala-based pentapeptide mimetics are BACE inhibitors: P2 and P3 SAR

Peptidomimetic Modulators of BACE1

The β-site APP Cleaving enzyme 1 (BACE1) is a membrane-associated aspartyl protease which mediates the production of amyloid-β (Aβ), a major component of amyloid plaques in the Alzheimer’s disease brain. We have synthesised and characterised a series of peptidomimetic analogues of BACE substrates that incorporate two distinct stabilising structures. To demonstrate the potential activity of these compounds, a variety of assaying strategies were used to investigate cleavage susceptibility and inhibition potency under competitive and non-competitive conditions. β-Amino acids and scissile site N-methylation were incorporated into peptide substrate templates as transition state isostere (TSI) substitutes by positional scanning to generate series of non-TSI β-peptidomimetics. The amino acid sequences flanking the β-cleavage site within APP carrying the Swedish double mutation (APPSW), Neuregulin, the synthetic hydroxyethylene-based TSI peptide inhibitor OM99-2, and the high affinity peptide sequence SEISYEVEFR, served as the four substrate templates from which over 60 peptides were designed and synthesised by solid phase peptide synthesis. A quenched fluorescent substrate BACE1 assay in conjunction with liquid chromatography–mass spectrometry (LC-MS) analysis was established to investigate cleavage susceptibility and inhibition potency under competitive and non-competitive conditions. It was determined that β-amino acids substituted at the P1 scissile site position within known peptide substrates were resistant to proteolysis, and particular substitutions induced a concentration-dependent stimulation of BACE1, indicating a possible modulatory role of native BACE1 substrates.

Cp*Rh(III)-Catalyzed C-H Bond Difluorovinylation of Indoles with α,α-Difluorovinyl Tosylate

Unprecedented Rh(III)-catalyzed C-H bond difluorovinylation of indoles has been successfully developed, and this method provided an example of direct difluorovinylation reaction through C-H bond activation which was rarely reported. In this context, N-ethoxycarbamoyl served as the directing group and 2,2-difluorovinyl tosylates were used for the construction of difluorovinyl-substituted indoles. This method provided a practical strategy for difluorovinylation of indoles with moderate to good yields and is characterized by the broad synthetic utility, mild conditions, and high efficiency.

Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor

The design and synthesis of potent, tripeptidic acylsulfonamide inhibitors of HCV NS3 protease that contain a difluoromethyl cyclopropyl amino acid at P1 are described. A cocrystal structure of 18 with a NS3/4A protease complex suggests the presence of a H-bond between the polarized C-H of the CHF₂ moiety and the backbone carbonyl of Leu135 of the enzyme. Structure-activity relationship studies indicate that this H-bond enhances enzyme inhibitory potency by 13- and 17-fold compared to the CH₃ and CF₃ analogues, respectively, providing insight into the deployment of this unique amino acid.

Pathogenic Aβ A2V versus protective Aβ A2T mutation: Early stage aggregation and membrane interaction

We investigated the effects of punctual A-to-V and A-to-T mutations in the amyloid precursor protein APP, corresponding to position 2 of Aβ1-42. Those mutations had opposite effects on the onset and progression of Alzheimer disease, the former inducing early AD pathology and the latter protecting against the onset of the disease. We applied Static and Dynamic Light Scattering and Circular Dichroism, to study the different mutants in the early stages of the aggregation process, essential for the disease. Comparative results showed that the aggregation pathways differ in the kinetics and extent of the process, in the size of the aggregates and in the evolution of the secondary structure, resulting in fibrils of different morphology, as seen by AFM. Mutated peptides had comparable toxic effects on N2a cells. Moreover, as assessed by X-ray scattering, all of them displayed disordering effects on the internal structure of mixed phospholipids-gangliosides model membranes.

Facile synthesis of mono- and bis-methylated Fmoc-Dap, -Dab and -Orn amino acids

A facile selective synthesis of mono and bis methylated Fmoc-Dap, -Dab and -Orn amino acids in a one-pot process.

Addition of electrophilic radicals to 2-benzyloxyglycals: synthesis and functionalization of fluorinated α-C-glycosides and derivatives

A new method for the synthesis of fluorinated α-C-glycosides is described. The reactions between highly electrophilic radicals (fluorinated or unfluorinated) and a 2-benzyloxyglucal or galactal provide 2-keto-D-arabino- or 2-keto-D-lyxo-hexopyranosides through an addition/fragmentation process. Sodium borohydride mediated or Meerwein-Ponndorf-Verley (MPV) reduction of these compounds provides α-C-glycosides that feature appropriate anchoring groups for further synthetic elaboration. The presence of CF2 CO2 iPr or CF2 Br groups at the pseudo-anomeric position allows efficient reduction/olefination or Br/Li-exchange/nucleophilic-addition sequences. These transformations open the way for the synthesis of fluorinated C-glycosidic analogues of glycoconjugates.

Advances in the identification of β-secretase inhibitors

INTRODUCTION

Alzheimer's disease (AD), which is characterized by progressive intellectual deterioration, is the most common cause of dementia. β-Secretase (or BACE1) expression is a trigger for amyloid β peptide formation, a cause of AD, and thus is a molecular target for the development of drugs against AD. Many BACE1 inhibitors have been identified by academic and pharmaceutical research groups and a number of advanced technologies in drug discovery have been applied to the drug discovery.

AREAS COVERED

The purpose of this review is to present and discuss the methodologies used for BACE1 inhibitor drug discovery via substrate- and structure-based design, high-throughput screening and fragment-based drug design. The authors also review the advantages and disadvantages of these methodologies.

EXPERT OPINION

Many BACE1 inhibitors have been designed using X-ray crystal structure-based drug design as well as through in silico screening. Nevertheless, there are serious problems with regards to deciding the best X-ray crystal structure for designing BACE1 inhibitors through computational approaches. There are two prominent configurations of BACE1 but there is still room for improvement. Future developments may make it possible to identify BACE1 inhibitors as potential drug candidates.

Effects of chain length and N-methylation on a cation-pi interaction in a beta-hairpin peptide

The effects of N-methylation and chain length on a cation-pi interaction have been investigated within the context of a beta-hairpin peptide. Significant enhancement of the interaction and structural stabilization of the hairpin have been observed upon Lys methylation. Thermodynamic analysis indicates an increased entropic driving force for folding upon methylation of Lys residues. Comparison of lysine to analogues ornithine (Orn) and diaminobutyric acid (Dab) indicates that lysine provides the strongest cation-pi interaction and also provides the most stable beta-hairpin due to a combination of side chain-side chain interactions and beta-sheet propensities. These studies have significance for the recognition of methylated lysine in histone proteins.

Multiwell fluorometric and colorimetric microassays for the evaluation of beta-secretase (BACE-1) inhibitors

The amyloid beta (Abeta) peptide is responsible for toxic amyloid plaque formation and is central to the aetiology of Alzheimer's disease (AD). It is generated by proteolytic processing of the amyloid precursor protein (APP) by beta-secretase (BACE-1) and gamma-secretase. Consequently, inhibition of BACE-1, a rate-limiting enzyme in the production of Abeta, is an attractive therapeutic approach to the treatment of Alzheimer's disease. This paper reports on improved microtiter plate-based fluorescence and colorimetric assays for the high-throughput screening (HTS) of BACE-1 inhibitors achieved by employing, for the first time, casein fluorescein isothiocyanate (casein-FITC) and N-alpha-benzoyl-D,L-arginine p-nitroanilide (BAPNA) as substrates, since they are known to be readily available and convenient substrates for proteases. The methods are based on the fluorescence enhancement following casein-FITC proteolysis and the visible absorbance of the p-nitroaniline (pNA) produced by BAPNA hydrolysis, with both reactions catalysed by BACE-1. Casein-FITC is a high-affinity substrate (K (m) = 110 nM) for BACE-1, more so than the Swedish (SW) type peptide (a peptide containing the Swedish mutant of APP, a familiar mutation that enhances Abeta production). BACE-1 catalysis of casein-FITC proteolysis exhibited Michaelis-Menten kinetic. Therefore, it was found that BACE-1 was saturable with casein-FITC that was processed in a time- and pH-dependent manner with greater catalytic efficiency than observed for the SW peptide. The enantioselective hydrolysis of L-BAPNA by BACE-1 was observed. L-BAPNA was hydrolysed ten times more efficiently by BACE-1 than the WT (wild-type peptide). The novel methods were validated using a FRET assay as an independent reference method. Therefore, in order to select new leads endowed with multifunctional activities, drugs for Alzheimer's disease (AD) - potent acetylcholinesterase (AChE) inhibitors - were tested for BACE-1 inhibition using the proposed validated assays. Among these, donepezil, besides being an acetylcholinesterase inhibitor, was also found to be a BACE-1 inhibitor that displayed submicromolar potency (170 nM).

Is inhibition of the renin-angiotensin system a new treatment option for Alzheimer's disease?

Findings from longitudinal and cross-sectional studies suggest an association between high blood pressure and dementia, and in turn the use of antihypertensives has been suggested to reduce incidence of dementia. Alzheimer's disease, the most common cause of dementia, is characterised in part by the deposition of amyloid beta protein (Abeta) in the brain. Reduction of Abeta load is now a major therapeutic strategy. In recent years the renin-angiotensin system, already of recognised importance in the pathogenesis of hypertension, has become a source of interest in the pathogenesis of Alzheimer's disease. This review explores molecular, genetic, and clinical studies that might help explain the relation between the renin-angiotensin system, hypertension, and Alzheimer's disease and whether treatment with angiotensin converting enzyme (ACE) inhibitors and similar treatment strategies have a part to play in the management of the disease.

Mapping of Interaction Domains Mediating Binding between BACE1 and RTN/Nogo Proteins

BACE1 is a membrane-bound aspartyl protease that specifically cleaves amyloid precursor protein (APP) at the beta-secretase site. Membrane bound reticulon (RTN) family proteins interact with BACE1 and negatively modulate BACE1 activity through preventing access of BACE1 to its cellular APP substrate. Here, we focused our study on RTN3 and further show that a C-terminal QID triplet conserved among mammalian RTN members is required for the binding of RTN to BACE1. Although RTN3 can form homo- or heterodimers in cells, BACE1 mainly binds to the RTN monomer and disruption of the QID triplet does not interfere with the dimerization. Correspondingly, the C-terminal region of BACE1 is required for the binding of BACE1 to RTNs. Furthermore, we show that the negative modulation of BACE1 by RTN3 relies on the binding of RTN3 to BACE1. The knowledge from this study may potentially guide discovery of small molecules that can mimic the effect of RTN3 on the inhibition of BACE1 activity.

Design, synthesis, and evaluation of Leu∗Ala hydroxyethylene-based non-peptide β-secretase (BACE) inhibitors

With the aim of developing small molecular non-peptide beta-secretase (BACE) inhibitors, Leu*Ala hydroxyethylene (HE) was investigated as a scaffold to design and synthesize a series of compounds. Taking advantage of efficient combinatorial synthesis approaches and molecular modeling, extensive structure-activity relationship (SAR) studies were carried out on the N- and C-terminal residues of the Leu*Ala HE scaffold. Isobutyl amine was found to be an optimal C-cap, and suitable hydroxylalkylamines at the 3-position and nitro or methyl(methylsulfonyl)amine at the 5-position of isophthalamide as the N-terminus could form additional hydrogen bonds with BACE active sites and help improve potency. Many new potent non-peptide BACE inhibitors were identified in this study. Among them, compounds 37 and 44 exhibited excellent enzyme-inhibiting potency, comparable to that of OM99-2, and obvious inhibitory effects in cell-based assay with low molecular weights (<600).

A novel approach to identifying beta-secretase inhibitors: bis-statine peptide mimetics discovered using structure and spot synthesis

Beta-secretase 1 (BACE1) is an aspartic protease believed to play a critical role in Alzheimer's disease. Inhibitors of this enzyme have been designed by incorporating the non-cleavable hydroxyethylene and statine isosteres into peptides corresponding to BACE1 substrate sequences. We sought to develop new methods to quickly characterize and optimize inhibitors based on the statine core. Minimal sequence requirements for binding were first established using both crystallography and peptide spot synthesis. These shortened peptide inhibitors were then optimized by using spot synthesis to perform iterative cycles of substitution and deletion. The present study resulted in the identification of novel "bis-statine" inhibitors shown by crystallography to have a unique binding mode. Our results demonstrate the application of peptide spot synthesis as an effective method for enhancing peptidomimetic drug discovery.

Synthesis of a novel conformationally restricted Val-Phe dipeptidomimetic

A method for the synthesis of (3(R,S),6S,11b(R,S))-1,3,4,6,7,11b-hexahydro-4-oxo-3-phthalimidopyrido[2,1-a]isoquinoline-6-carboxylic acid 2 as a new conformationally restricted dipeptidomimetic of Val-Phe is reported. It involved cyclisation via an intramolecular electrophilic addition at the reactive bridgehead carbon. This new scaffold can be used as a building block in the preparation of libraries of peptidomimetics.

Macrocyclic peptidomimetic inhibitors of beta-secretase (BACE): first X-ray structure of a macrocyclic peptidomimetic-BACE complex

The synthesis of novel macrocyclic peptidomimetic inhibitors of the enzyme BACE1 is described. These macrocycles are derived from a hydroxyethylene core structure. Compound 7 was co-crystallized with BACE1 and the X-ray structure of the complex elucidated at 1.6 Angstrom resolution. This molecule inhibits the production of the Abeta peptide in HEK293 cells overexpressing APP751sw.

Design and characterization of a new cell-permeant inhibitor of the beta-secretase BACE1

1 The beta-secretase BACE1 is one of the enzymes that contribute to the production of the Abeta peptide, in vitro and in vivo. JMV1195 was previously shown to inhibit BACE activity in vitro but was unable to block cellular BACE activity. We have designed a new permeable inhibitor, JMV2764 that corresponds to a derivative of JMV1195 to which a penetratin sequence had been added at its N-terminus. We have assessed the ability of JMV2764 to affect BACE1 activity in vitro, and to modify Abeta production in various cell systems. 2 Endogenous beta-secretase or BACE1 activities were monitored in vitro by means of two distinct fluorimetric substrates in HEK293 extracts of cells expressing either wild-type betaAPP, Swedish mutated betaAPP or SPA4CT constructs. Abeta40 recovery was monitored by immunoprecipitation and Western blot analysis. 3 JMV2764 and JMV1195 inhibited endogenous beta-secretase activity of HEK293 cellular homogenates with IC(50)s of 0.8 and 6.6 microM, respectively. Interestingly, JMV2764 also inhibited beta-secretase activity after preincubation with intact cells while JMV1195 was inactive, indicating that unlike JMV1195, JMV2764 could penetrate into the cells. 4 JMV2764 but not JMV1195 also prevented Abeta production by HEK293 cells overexpressing wild-type and Swedish-mutated betaAPP. However, JMV2764 was unable to affect Abeta production from cells expressing SPA4CT, a betaAPP-derived sequence that does not need beta-secretase to produce Abeta. 5 Altogether, we have designed a new cell-permeable BACE1 inhibitor that allows to envision to prevent Abeta production in vivo. Work is in progress to assess the potential of these compounds to prevent Abeta production in transgenic mice overproducing Abeta.

Biochemical and cell-based assays for characterization of BACE-1 inhibitors

The deposition of beta-amyloid peptides (A beta42 and A beta40) in neuritic plaques is one of the hallmarks of Alzheimer's disease (AD). A beta peptides are derived from sequential cleavage of amyloid precursor protein (APP) by beta- and gamma-secretases. BACE-1 has been shown to be the major beta-secretase and is a primary therapeutic target for AD. In this article, two novel assays for the characterization of BACE-1 inhibitors are reported. The first is a sensitive 96-well HPLC biochemical assay that uses a unique substrate containing an optimized peptide cleavage sequence, NFEV, spanning from the P2-P2' positions This substrate was processed by BACE-1 approximately 10 times more efficiently than was the widely used substrate containing the Swedish (NLDA) sequence. As a result, the concentration of the enzyme required for the assay can be as low as 100 pM, permitting the evaluation of inhibitors with subnanomolar potency. The assay has also been applied to related aspartyl proteases such as cathepsin D (Cat D) and BACE-2. The second assay is a homogeneous electrochemiluminescence assay for the evaluation of BACE-1 inhibition in cultured cells that assesses the level of secreted amyloid EV40_NF from HEK293T cells stably transfected with APP containing the novel NFEV sequence. To illustrate the use of these assays, the properties of a potent, cell-active BACE-1 inhibitor are described.

Compounds that bind APP and inhibit Abeta processing in vitro suggest a novel approach to Alzheimer disease therapeutics

Extracellular deposits of aggregated amyloid-beta (Abeta) peptides are a hallmark of Alzheimer disease; thus, inhibition of Abeta production and/or aggregation is an appealing strategy to thwart the onset and progression of this disease. The release of Abeta requires processing of the amyloid precursor protein (APP) by both beta- and gamma-secretase. Using an assay that incorporates full-length recombinant APP as a substrate for beta-secretase (BACE), we have identified a series of compounds that inhibit APP processing, but do not affect the cleavage of peptide substrates by BACE1. These molecules also inhibit the processing of APP and Abeta by BACE2 and selectively inhibit the production of Abeta(42) species by gamma-secretase in assays using CTF99. The compounds bind directly to APP, likely within the Abeta domain, and therefore, unlike previously described inhibitors of the secretase enzymes, their mechanism of action is mediated through APP. These studies demonstrate that APP binding agents can affect its processing through multiple pathways, providing proof of concept for novel strategies aimed at selectively modulating Abeta production.

Apo and inhibitor complex structures of BACE (beta-secretase)

Human BACE, also known as beta-secretase, shows promise as a potential therapeutic target for Alzheimer's disease. We determined the apo structure of BACE to 1.75 A, and a structure of a hydroxyethylamine inhibitor complex derived by soaking. These show significant active-site movements compared to previously described BACE structures. Additionally, the structures reveal two pockets that could be targeted by structure-based drug design.

P3 cap modified Phe*-Ala series BACE inhibitors

With the aim of reducing molecular weight and adjusting log D value of BACE inhibitors to more favorable range for BBB penetration and better bioavailability, we synthesized and evaluated several series of P3 cap modified BACE inhibitors obtained via replacement of the P3NHBoc moiety as seen in 3 with other polar functional groups such as amino, hydroxyl and fluorine. Several promising inhibitors emerging from this P3 cap SAR study (e.g., 15 and 19) demonstrated good enzyme inhibitory potencies (BACE-1 IC(50) <50 nM) and whole cell activities (IC(50) approximately 1 microM).