Publications by Yimon Aye | EPFL Graph Search

Related publications (48)

Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox responses in larval fish

This Protocol Extension describes the adaptation of an existing Protocol detailing the use of targetable reactive electrophiles and oxidants, an on-demand redox targeting toolset in cultured cells. The adaptation described here is for use of reactive elect ...

NATURE PORTFOLIO2023

Breaking the Fourth Wall: Modulating Quaternary Associations for Protein Regulation and Drug Discovery

Yimon Aye, Bokyoung Kim

Protein-protein interactions (PPIs) are an effective means to orchestrate intricate biological processes required to sustain life. Approximately 650000 PPIs underlie the human interactome; thus underscoring its complexity and the manifold signaling outputs ...

WILEY-V C H VERLAG GMBH2019

Electrophile Signaling and Emerging Immuno- and Neuro-modulatory Electrophilic Pharmaceuticals

Yimon Aye, Jesse Poganik

With a lipid-rich environment and elevated oxygen consumption, the central nervous system (CNS) is subject to intricate regulation by lipid-derived electrophiles (LDEs). Investigations into oxidative damage and chronic LDE generation in neural disorders ha ...

FRONTIERS MEDIA SA2020

Getting the Right Grip? How Understanding Electrophile Selectivity Profiles Could Illuminate Our Understanding of Redox Signaling

Yimon Aye, Lingxi Wang

Recent Advances: Herein, we focus on the first step of this process, electrophile sensing. Electrophile sensing is typically a deceptively simple reaction between the thiol of a protein cysteine, of which there are around 200,000 in the human proteome, and ...

MARY ANN LIEBERT, INC2020

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

REX technologies for profiling and decoding the electrophile signaling axes mediated by Rosetta Stone proteins

Daniel Ahmet Urul, Yimon Aye

It is now clear that some cysteines on some proteins are highly tuned to react with electrophiles. Based on numerous studies, it is also established that electrophile sensing underpins rewiring of several critical signaling processes. These electrophile-se ...

ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD2020

Hitting the Bullseye: Endogenous Electrophiles Show Remarkable Nuance in Signaling Regulation

Pierre Alexander Miranda Herrera, Yimon Aye

Our bodies produce a host of electrophilic species that can label specific endogenous proteins in cells. The signaling roles of these molecules are under active debate. However, in our opinion, it is becoming increasingly likely that electrophiles can rewi ...

AMER CHEMICAL SOC2022

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

Yimon Aye, Chloé Rogg

Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...

WILEY-V C H VERLAG GMBH2023

The not so identical twins: (dis)similarities between reactive electrophile and oxidant sensing and signaling

Yimon Aye, Kuan-Ting Huang

In this tutorial review, we compare and contrast the chemical mechanisms of electrophile/oxidant sensing, and the molecular mechanisms of signal propagation. We critically analyze biological systems in which these different pathways are believed to be mani ...

Royal Society of Chemistry2021

The mRNA-Binding Protein HuR Is a Kinetically-Privileged Electrophile Sensor

Yimon Aye, Jesse Poganik, Alexandra Krina Van Hall-Beauvais, Yi Zhao

The key mRNA-binding proteins HuR and AUF1 are reported stress sensors in mammals. Intrigued by recent reports of sensitivity of these proteins to the electrophilic lipid prostaglandin A2 and other redox signals, we here examined their sensing abilities to ...

2020

Monitoring On-Target Signaling Responses in Larval Zebrafish- Z-REX Unmasks Precise Mechanisms of Electrophilic Drugs and Metabolites

Yimon Aye, Jesse Poganik, Kuan-Ting Huang, Phillippe Ly

Reactive metabolites and related electrophilic drugs are among the most challenging small molecules to study. Conventional approaches to deconstruct the mode of action (MOA) of such molecules leverage bulk treatment of experimental specimens with an excess ...

JOURNAL OF VISUALIZED EXPERIMENTS2023

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Yimon Aye, Alexandra Krina Van Hall-Beauvais

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of `omics', we discuss what makes the larger subunit o ...

ELSEVIER SCI LTD2020

Finding a vocation for validation: taking proteomics beyond association and location

Yimon Aye, Jinmin Liu

First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision- ...

ROYAL SOC CHEMISTRY2022

A primer on harnessing non-enzymatic post-translational modifications for drug design

Yimon Aye, Phillippe Ly

Of the manifold concepts in drug discovery and design, covalent drugs have re-emerged as one of the most promising over the past 20-or so years. All such drugs harness the ability of a covalent bond to drive an interaction between a target biomolecule, typ ...

ROYAL SOC CHEMISTRY2021

Empowering Global Chemical Biology at the Dawn of the New Decade

Yimon Aye

On January 22-24, 2020, scientific luminaries across the far-flung corners of chemical biology gathered in Geneva, Switzerland, to deliver their latest and greatest discoveries in the field. Generously supported by the Swiss National Science Foundation (SN ...

AMER CHEMICAL SOC2020

Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity

Yimon Aye, Xuyu Liu

Here we discuss, how by applying chemical concepts to biological problems, methods have been developed to map spatiotemporal regulation of proteins and small-molecule modulation of proteome signaling responses. We outline why chemical-biology platforms are ...

2019

Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1

Yimon Aye, Xuyu Liu, Jesse Poganik

The nuclear factor erythroid 2 related factor 2 (Nrf2) signaling axis is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of Nrf2 regulation has been focused at the protein level. Here we report a post-trans ...

FEDERATION AMER SOC EXP BIOL2019

Precision Targeting of pten-Null Triple-Negative Breast Tumors Guided by Electrophilic Metabolite Sensing

Chaosheng Luo, Yimon Aye, Xuyu Liu, Lingxi Wang

Off-target effects continue to impede disease interventions, particularly when targeting a specific protein within a family of similar proteins, such as kinase isoforms that play tumor-subtype-specific roles in cancers. Exploiting the specific electrophili ...

AMER CHEMICAL SOC2020

Bringing Functional Context to Emerging Proximity-mapping Proteomics Tools

Yimon Aye

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current st ...

SWISS CHEMICAL SOC2022

Genie in a bottle: controlled release helps tame natural polypharmacology?

Yimon Aye, Xuyu Liu

Ability to faithfully report drug-target interactions constitutes a major critical parameter in preclinical/clinical settings. Yet the assessment of target engagement remains challenging, particularly for promiscuous and/or polypharmacologic ligands. Drawi ...

2019