Structural basis of γ-secretase inhibition and modulation by small molecule drugs

Yang, Guanghui; Zhou, Rui; Guo, Xuefei; Yan, Chuangye; Lei, Jianlin; Shi, Yigong

doi:10.1016/j.cell.2020.11.049

Cited by 133 publications

(201 citation statements)

References 87 publications

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“…This region has been suggested to be important for substrate recognition and proteolytic processing (12). Similarly, g-secretase inhibitors (GSIs) and transition state analogs (TSAs) bind to this region (28). Pep-GaMD could show important atomistic dynamism of this region during the enzyme activation for z cleavage.…”

Section: Discussionmentioning

confidence: 99%

“…Yet the mechanism of processive proteolysis of APP by γ-secretase is unknown. Recent reports of cryo-EM structures of γ-secretase bound to APP and Notch substrates as well as to γ-secretase inhibitors and modulators revealed details of the structural basis of substrate recognition as well as enzyme inhibition and modulation (11,12,30). Regardless, static conformations of the enzyme cannot explain the underlying mechanism of enzyme activation and substrate processing.…”

Section: Discussionmentioning

confidence: 99%

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Mechanism of Tripeptide Trimming by γ-Secretase

Bhattarai

Devkota

Nguyen

et al. 2021

Preprint

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The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer’s disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and western blotting were used to quantify the efficiency of the first tripeptide trimming step (Aβ49→Aβ46) of wildtype (WT) and familial AD (FAD) mutant APP substrate. In comparison to WT APP, the efficiency of this first trimming step was slightly higher for the I45F, A42T and V46F APP FAD mutants, but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate tripeptide trimming of Aβ49 by γ-secretase. The starting structure was active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai et al., ACS Cent Sci, 2020, 6:969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming by γ-secretase.Significance statementProduction of amyloid β-peptide (Aβ) of Alzheimer’s disease (AD) from its precursor protein requires a series of proteolytic events carried out by the membrane-embedded γ-secretase complex. Mutations in the substrate and enzyme that produce Aβ cause hereditary AD and these mutations affect tripeptide trimming of initially formed long Aβ peptides by γ-secretase. Little is known about the structural mechanism of this trimming process. Here we have developed a molecular dynamics model for the first step of trimming (Aβ49 to Aβ46) by γ-secretase. Conformational changes in the enzyme-substrate complex to set up this trimming step require the presence of N-terminally charged endoproteolytic cleavage co-product. Computational effects of AD-causing mutations in Aβ49 on the trimming process were validated through biochemical experiments.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Mechanism of Tripeptide Trimming by γ-Secretase

Bhattarai

Devkota

Nguyen

et al. 2021

Preprint

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“…One such substrate is the notch protein, which regulates cell growth, differentiation, and communication [40]. Inhibitors of γsecretase, such as Semagacestat and Avagacestat, have not been approved for marketing because the former caused significant adverse reactions such as cognitive decline and decreased ability to perform daily activities, and the latter was ineffective [41]. To avoid the negative effects of overall enzyme inhibition, selective γ-secretase modulators (SGSM) could be developed [42].…”

Section: Beta and Gamma Secretase Inhibitionmentioning

confidence: 99%

The Role of Polyphenols in the Treatment of Alzheimer's Disease: Narrative Review

Alattiya

Tarish

Hashim

et al. 2021

Al-Rafidain J Med Sci

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Many epidemiological studies have suggested that consuming a diet rich in polyphenols can help prevent Alzheimer's disease (AD). Based on well-known in vitro and in vivo models of cerebral Aβ amyloidosis, we examined the data on the effects of various natural polyphenols on the aggregation of amyloid-protein (Aβ). These polyphenols effectively prevent oligomerization and fibril formation of Aβ through differential binding patterns, lowering Aβ oligomer-induced synaptic and neuronal toxicity, according to in vitro investigations. Furthermore, in a transgenic mouse model fed orally with such polyphenolic compounds, soluble Aβ oligomers as well as insoluble Aβ deposits in the brain were significantly reduced. Natural polyphenols exhibit anti-amyloidogenic effects on Aβ, in addition to well-known anti-oxidative and anti-inflammatory activities, according to an updated assessment of the literature, implying their potential as therapeutic and/or preventive agents for AD treatment. To prove polyphenols' efficacy as disease-modifying agents, well-designed clinical trials or preventive treatments using various polyphenols are required.

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“…28 Recent structure elucidation of the protease bound to two non-transition inhibitors and former clinical candidates semagacestat and avagacestat revealed interaction with this same β-strand-forming region of PSEN1. 30 As avagacestat has shown some selectivity for inhibiting γ-secretase cleavage of APP vis-à-vis Notch, a better understanding of the nature of this particular substrate-enzyme interaction may facilitate structure-based design of agents with improved selectivity for APP. Table 1.…”

Section: Structure-activity Relationshipsmentioning

confidence: 99%

“…Most recently, structures of active enzyme bound to several inhibitors and to a modulator were also solved. 30 Despite these advances, structural understanding of the multiple steps in substrate recognition and processive proteolysis in the lipid bilayer remains largely unclear. Our goal was to engineer a new class of inhibitors based on an entire substrate TMD, to trap the active enzyme in a conformation poised for TMD hydrolysis for study by cryo-EM.…”

Section: Introductionmentioning

confidence: 99%

Design of Transmembrane Mimetic Structural Probes to Trap Different Stages of γ-Secretase-Substrate Interaction

Bhattarai

Devkota

Wolfe

2021

Preprint

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ABSTRACTγ-Secretase, a membrane-embedded aspartyl protease complex with presenilin as the catalytic component, cleaves within the transmembrane domain (TMD) of its many substrates, which include the amyloid precursor protein (APP) of Alzheimer’s disease (AD). APP TMD is processively cut by γ-secretase through endoproteolysis followed by tricarboxypeptidase “trimming”, the latter function being deficient with mutations causing hereditary AD. Toward better understanding of substrate recognition and hydrolytic reactions catalyzed by this enzyme within its hydrophobic milieu, we recently developed a prototype substrate TMD mimetic as a chemical tool for structural analysis (Bhattarai S et al. J. Am. Chem. Soc., 2020, 142(7): 3351-3355). This TMD mimetic—composed of a helical peptide inhibitor (HPI) connected through a linker to a transition-state analog inhibitor (TSA)— simultaneously engages the substrate docking exosite and the active site and is pre-organized to trap the protease transition state of carboxypeptidase trimming. In this study, we developed variants of this prototype designed to allow visualization of transition states for endoproteolysis, TMD helix unwinding, and lateral gating of substrate. New HPI-TSA conjugates were synthesized using an earlier established divergent strategy, which involved the construction of a tripeptidomimetic building block followed by solid-phase peptide synthesis (SPPS). For each class of structural probe, SAR analysis led to discovery of highly potent prototypes with stoichiometric or low-nanomolar inhibition. These TMD mimetics exhibited non-competitive inhibition of γ-secretase activity and occupy both docking and active site as demonstrated by enzyme cross competition experiments and photoaffinity probe binding assays. The new probes should be important structural tools for trapping different stages of substrate recognition and processing via ongoing cryo-electron microscopy with γ-secretase, ultimately aiding rational drug design.Abstract Graphic

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Structural basis of γ-secretase inhibition and modulation by small molecule drugs

Cited by 133 publications

References 87 publications

Mechanism of Tripeptide Trimming by γ-Secretase

Mechanism of Tripeptide Trimming by γ-Secretase

The Role of Polyphenols in the Treatment of Alzheimer's Disease: Narrative Review

Design of Transmembrane Mimetic Structural Probes to Trap Different Stages of γ-Secretase-Substrate Interaction

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