Biology subjects

Habchi, J.

Publications and source records attributed to Habchi, J..

6 recordsLinked to original sources

bioRxiv2023

Molecular mechanism of α-synuclein aggregation on lipid membranes revealed.

The central hallmark of Parkinsons disease pathology is the aggregation of the -synuclein protein, which, in its healthy form, is associated with lipid membranes. Purified monomeric -synuclein is relatively stable in vitro, but its aggregation can be triggered by the presence of lipid vesicles. Despite this central importance of lipids in the context of -synuclein aggregation, their mechanistic role in this process has not been established to date. Here, we use chemical kinetics to develop a detailed mechanistic model that is able to globally describe the aggregation behaviour of -synuclein in the presence of DMPS lipid vesicles, across a range of lipid and protein concentrations. Through the application of our kinetic model to experimental data, we find that the reaction is a co-aggregation process involving both protein and lipids and that lipids promote aggregation predominantly by enabling the elongation process. Moreover, we find that the initial formation of aggregates, via primary nucleation, takes place not on the surface of lipid vesicles but at the interfaces present in vitro. Our model will enable mechanistic insights, also in other lipid-protein co-aggregation systems, which will be crucial in the rational design of drugs that inhibit aggregate formation and act at the key points in the -synuclein aggregation cascade.

biophysics↗

bioRxiv2021

Structure-based discovery of small molecule inhibitors of the autocatalytic proliferation of alpha-synuclein aggregates

The presence of amyloid fibrils of -synuclein is closely associated with Parkinsons disease and related synucleinopathies. It is still very challenging, however, to systematically discover small molecules that prevent the formation of these aberrant aggregates. Here, we describe a structure-based approach to identify small molecules that specifically inhibit the surface-catalyzed secondary nucleation step in the aggregation of -synuclein by binding to the surface of the amyloid fibrils. The resulting small molecules are screened using a combination of kinetic and thermodynamic assays for their ability to bind -synuclein fibrils and prevent the further generation of toxic oligomers. This study demonstrates that the combination of structure-based and kinetic-based drug discovery methods can lead to the identification of small molecules that selectively inhibit the autocatalytic proliferation of -synuclein aggregates.

biophysics↗

bioRxiv2021

A Machine Learning Approach to Identify Specific Small Molecule Inhibitors of Secondary Nucleation in alpha-Synuclein Aggregation

Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where the development of disease-modifying drugs has been particularly challenging. To address this problem, we describe here a machine learning approach to identify small molecule inhibitors of -synuclein aggregation, a process implicated in Parkinsons disease and other synucleinopathies. Because the proliferation of -synuclein aggregates takes place through autocatalytic secondary nucleation, we aim to identify compounds that bind the catalytic sites on the surface of the aggregates. To achieve this goal, we use structure-based machine learning in an iterative manner to first identify and then progressively optimize secondary nucleation inhibitors. Our results demonstrate that this approach leads to the facile identification of compounds two orders of magnitude more potent than previously reported ones.

biophysics↗

bioRxiv2021

Vitamin A and vitamin E metabolites comodulate amyloid-β aggregation

Alzheimers disease is characterized by the presence in the brain of amyloid plaques formed by the aberrant deposition of the amyloid-{beta} peptide (A{beta}). Since many vitamins are dysregulated in this disease, we explored whether these molecules participate in protein homeostasis by modulating A{beta} aggregation. By screening 18 fat-soluble and water-soluble vitamins, we found that retinoic acid and -tocopherol, two metabolites of vitamin A and vitamin E, respectively, affect A{beta} aggregation both in vitro and in a C. elegans model of Alzheimers disease. We also show that effects of these two vitamin metabolites in combination can cancel each other out, suggesting that the complex composition of the cellular environment could have a protective role against protein aggregation through the simultaneous presence of aggregation promoters and inhibitors. Taken together, these results indicate that vitamins and their metabolites may be added to the list of components of the quality control system that regulate protein aggregation.

biophysics↗

bioRxiv2020

Infrared Nanospectroscopy Reveals the Molecular Interaction Fingerprint of an Aggregation Inhibitor with Single Aβ42 Oligomers

Very significant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimers and Parkinsons diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule level morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the interaction between single A{beta}42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, originally an anticancer drug capable recently shown to be able to inhibit A{beta}42 aggregation in animal models of Alzheimers disease. Our results demonstrate that the carbonyl group of this compound interacts with A{beta}42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as powerful tool in structure-based drug discovery for protein misfolding diseases.

biophysics↗

bioRxiv2018

Conformational footprinting of proteins using a combination of top-down electron transfer dissociation and ion mobility

In recent years native mass spectrometry has been increasingly employed to study protein structure. As such a thorough understanding of the effect of the gas-phase on protein structure is becoming increasingly important. We show how a combination of top-down ETD and ion mobility can be used to probe the gas-phase structure of heterogeneous protein ensembles. By applying collisional activation to the non-covalently bound ETD products after IM separation, the peptide fragments can be released while maintaining the conformational information of the protein ion. We studied the unknown gas-phase structures of the measles virus (MeV) phosphoprotein X domain (PXD), which shows a wide range of different conformations in the gas-phase. We then generated structural models by state-of-the-art gas-phase steered molecular dynamics, which we verified using restraints from ion mobility and the fragment patterns observed. Our findings illustrate the applicability of ETD for obtaining conformational specific structural information on heterogeneous protein ensembles.

biophysics↗