Biology subjects

D'Amore, V. M.

Publications and source records attributed to D'Amore, V. M..

3 recordsLinked to original sources

bioRxiv2026

Sephin1 rewires proteostasis through actin-dependent signaling

The maintenance of protein homeostasis is vital for all cells. Alteration in protein handling underlies several diseases. The small molecule sephin1 is a promising clinical candidate against proteostasis disruption, but its mechanism of action is still uncertain. Our experimental evidence shows that sephin1 binds G-actin and drives actin cytoskeleton misfolding, and eventually, Golgi disintegration. At first, sephin1 impairs the autophagic flux and elicits the phosphorylation of the subunit of eIF2 and the ER-stress independent expression of CHOP via GCN2 kinase. Sephin1 also inhibits the mammalian target of rapamycin (mTORC1), activates the transcription Factor EB (TFEB), drives the expression of TFEB-direct target genes, and eventually stimulates the autophagy lysosomal pathway. Our results reveal that the actin cytoskeleton may regulate autophagy via mTORC1-TFEB complemented with the GCN2-eIF2-CHOP signaling pathway.

cell biology↗

bioRxiv2025

Ligand-Induced Structural Dynamics Drive Allosteric Regulation of Translation Initiation Factor eIF4E

The eukaryotic initiation factor 4E (eIF4E) governs cap-dependent translation, and its dysregulation contributes both to cancer and neurological disorders, making it an attractive target for therapeutic intervention. Among the few small-molecule inhibitors developed, 4EGI-1 and its analogue i4EG-BiP have shown promise in cellular and preclinical models. These compounds disrupt eIF4Es interaction with its partner eIF4G while enhancing binding to its negative regulators, the 4E-binding proteins (4E-BPs). Despite their chemical similarity and overlapping functional effects, structural data suggest the two ligands engage different regions of eIF4E, lateral for 4EGI-1 and frontal for i4EG-BiP, raising questions about the basis of their shared activity. Here, we integrate molecular simulations, site-directed mutagenesis, and fluorescence binding assays to elucidate the mechanism of action of both ligands. Funnel metadynamics free-energy calculations reveal that the frontal binding mode is thermodynamically preferred for both compounds. Furthermore, we demonstrate that the conformational rearrangement induced by frontal binding selectively promotes 4E-BP1 over eIF4G association, explaining their common allosteric regulatory effect. These findings reconcile divergent structural observations and highlight how ligand-induced dynamics can be exploited to reprogram eIF4E interactions, offering a framework for next-generation therapeutics targeting dysregulated translation.

molecular biology↗

bioRxiv2023

Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveals a receptor pseudo-active state

G protein coupled receptors (GPCRs) are membrane proteins of greatest pharmacological relevance, targeted by over one third of marketed drugs. These receptors are activated by orthosteric ligands and undergo large conformational changes that lead to coupling diverse effector proteins. To achieve a fine regulation of the drug pharmacological response, it is imperative to shed light on the yet poorly understood aspects of GPCRs activation. In this work, we elucidate the entire activation mechanism of the adenosine A2A receptor (A2AR), a class A GPCR, performing minute timescale molecular dynamics and free energy calculations. We have explored the entire conformational landscape of A2AR in its basal apo form and in differently ligated conditions, elucidating the ligand intrinsic activity and the receptors lowest energy functional states. Among these is a novel pseudo-active state (pAs) of the A2AR apo form stabilised by specific "microswitch" residues interactions, including the salt bridge between the class A conserved residues R5.66 and E6.30. In the pAs state, A2AR is able to couple {beta}-arrestin 1 over G proteins, providing unprecedented structural basis for receptor desensitization and G protein-alternative cellular pathways. Our simulation protocol is generalisable and can be applied to study the activation of any GPCR, resulting a precious tool for drug design and biased signaling studies.

biophysics↗