Publications by Yimon Aye | EPFL Graph Search

Horner-Wadsworth-Emmons olefination for bioconjugation

Through site-specific generation of intermediary reactive aldehydes, Horner-Wadsworth-Emmons olefination can now deliver selective functionalization of stable recombinant proteins and monoclonal antibodies, whilst preserving protein integrity. ...

Springernature2024

Toward decoding spatiotemporal signaling activities of reactive immunometabolites with precision immuno-chemical biology tools

Yimon Aye, Kuan-Ting Huang

Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs—e.g., fumarate, itaconate) is an emerging phenomenon of major biomedical importance. Despite their localized production, mt-REMs elicit significantly ...

2024

Let's get biophysical - How to get your favorite protein's digits☆

Yimon Aye

In these days of information overload and high-throughput analysis, it is easy to lose focus on the study of individual proteins. It is our conjecture that such investigations are still crucially important and offer uniquely penetrative insights. We thus p ...

PERGAMON-ELSEVIER SCIENCE LTD2024

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

Formaldehyde regulates one-carbon metabolism and epigenetics

Yimon Aye

Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...

Cell Press2024

Tag, you're it: G-ICAT identifies p120-cysteine glutathionylation triggering E-cadherin destabilization

Yimon Aye

Current methods have limited ability in directly quantifying the extent of glutathionylation on specific proteincysteines. In this issue of Cell Chemical Biology, Ahn et al.1 report G-ICAT (glutathione-based isotope-coded affinity tag), aimed at addressing ...

CELL PRESS2023

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

Chloé Rogg, Yimon Aye

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

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

Yimon Aye, Kuan-Ting Huang, Sruthi Raja

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

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

Keap It in the Family: How to Fish out New Paradigms in Keap1-Mediated Cell Signaling

Yimon Aye, Kuan-Ting Huang

Keap1 is associated with cytoprotective signaling. These roles of Keap1 typically focus on its role as a degrader of the antioxidant response (AR) transcription factor, Nrf2, and the inhibition of this process upon Keap1 labeling by electrophiles. However, ...

Wiley-V C H Verlag Gmbh2023

Z-REX uncovers a bifurcation in function of Keap1 paralogs

Yimon Aye, Xuyu Liu, Jesse Poganik, Alexandra Krina Van Hall-Beauvais, Yi Zhao, Kuan-Ting Huang

Studying electrophile signaling is marred by difficulties in parsing changes in pathway flux attributable to on-target, vis-& agrave;-vis off-target, modifications. By combining bolus dosing, knockdown, and Z- REX & mdash;a tool investigating on- target/on ...

eLIFE SCIENCES PUBL LTD2022

Can Precision Electrophile Signaling Make a Meaningful and Lasting Impression in Drug Design?

Yimon Aye, Amogh Kulkarni

For several years, drugs with reactive electrophilic appendages have been developed. These units typically confer prolonged residence time of the drugs on their protein targets, and may assist targeting shallow binding sites and/or improving the drug-prote ...

WILEY-V C H VERLAG GMBH2022

Hiding in Plain Sight: The Issue of Hidden Variables

Yimon Aye, Mahdi Assari

Here we discuss "hidden variables", which are typically introduced during an experiment as a consequence of the application of two independent variables together to create a stimulus. With increased sophistication in modern chemical biology tools and relat ...

AMER CHEMICAL SOC2022

Function-guided proximity mapping unveils electrophilic-metabolite sensing by proteins not present in their canonical locales

Romain Hamelin, Yimon Aye, Yi Zhao, Pierre Alexander Miranda Herrera

Enzyme-assisted posttranslational modifications (PTMs) constitute a major means of signaling across different cellular compartments. However, how nonenzymatic PTMs-despite their direct relevance to covalent drug development-impinge on crosscompartment sign ...

National Academy of Sciences2022

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

Yimon Aye, Pierre Alexander Miranda Herrera

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

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

Jinmin Liu, Yimon Aye

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

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

Keap 1: The new Janus word on the block

Yimon Aye

Here we draw insights from the latest serendipitous findings made on the opposing roles of a proposed drug-target protein Keap1. We weigh up how natural reactive electrophiles and electrophilic small-molecule drugs in clinical use directly impinge on seemi ...

PERGAMON-ELSEVIER SCIENCE LTD2022

Go to the Board: A Journey through the Life of Professor David A. Evans

Yimon Aye

By taking a journey through the events that happened during Professor David A. Evans' lifetime in the context of chemical synthesis and drug discovery, this in-focus article reflects upon Professor Evans' lifelong scientific and padegogical impacts on the ...

AMER CHEMICAL SOC2022

An Oculus to Profile and Probe Target Engagement In Vivo: How T-REX Was Born and Its Evolution into G-REX

Chloé Rogg, Yimon Aye

Here we provide a personal account of innovation and design principles underpinning a method to interrogate precision electrophile signaling that has come to be known as "REX technologies". This Account is framed in the context of trying to improve methods ...

AMER CHEMICAL SOC2021