---
title: "Chemical Proteomics Maps the Cholesteryl Ester Interactome in Mammalian Cells"
id: "biorxiv-22-orthogonal-chemical-proteomic-strategies-reveal-the-cholesteryl-ester"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-22-orthogonal-chemical-proteomic-strategies-reveal-the-cholesteryl-ester"
content_type: "clinical_feed_article"
specialty: "Pharmacology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1?rss=1"
published_at: "2026-09-23T09:50:14.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Chemical Proteomics Maps the Cholesteryl Ester Interactome in Mammalian Cells
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-22-orthogonal-chemical-proteomic-strategies-reveal-the-cholesteryl-ester
- **Specialty:** [Pharmacology](https://medichelpline.com/clinical-feed/pharmacology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1?rss=1)
- **Published At:** 2026-09-23T09:50:14.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The study establishes an integrated **chemical proteomic** platform to define interactions between **cholesteryl esters (CEs)** and proteins in mammalian cells. - Three orthogonal **photoaffinity labeling** strategies were developed and compared: metabolic assembly of a bifunctional CE probe via endogenous acyltransferase activity, direct delivery of a diazirine-alkyne CE analog, and fragment-assisted subtraction using sterol and fatty acyl control probes. - Each probe system was validated with lipidomics and UV-dependent crosslinking before quantitative proteomic analysis. - Integration of the three complementary modalities identified **495 CE-associated proteins**, including enzymes, transporters, scaffolding proteins, and canonical sterol-binding families. - There was limited overlap in protein hits across the three strategies, indicating that **lipid-protein engagement** depends on biosynthetic origin, probe topology, and intracellular routing. - Functional and database annotations showed enrichment of **druggable** and **disease-linked** proteins, linking CE interactions to metabolic, neurological, and cardiovascular pathways. - The work provides the first systems-level map of CE-protein interactions and presents a generalizable multimodal framework for chemically resolving lipid-protein interactomes. - This article is a preprint and has not been peer reviewed; additional experimental details and the full protein lists are provided in the manuscript and supplementary material but are not reproduced here.
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Aakash Chandramouli 1 IISER Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Aakash%2BChandramouli%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Chandramouli%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAakash%2BChandramouli%2B) Kavita Sharma 2 Indian Institute of Science Education and Research (IISER) Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Kavita%2BSharma%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Sharma%20K&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AKavita%2BSharma%2B) Adithya Kallattu 1 IISER Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Adithya%2BKallattu%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kallattu%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAdithya%2BKallattu%2B) Chaitanya Katkar 1 IISER Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Chaitanya%2BKatkar%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Katkar%20C&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AChaitanya%2BKatkar%2B) Manish Deshmukh 1 IISER Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Manish%2BDeshmukh%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Deshmukh%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AManish%2BDeshmukh%2B) Pooja Thakral 1 IISER Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Pooja%2BThakral%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Thakral%20P&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3APooja%2BThakral%2B) Harinath Chakrapani 3 Indian Institute of Science Education and Research * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Harinath%2BChakrapani%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Chakrapani%20H&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AHarinath%2BChakrapani%2B) * [ORCID record for Harinath Chakrapani](http://orcid.org/0000-0002-7267-0906 "Open in new tab") Siddhesh S Kamat 2 Indian Institute of Science Education and Research (IISER) Pune; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Siddhesh%2BS%2BKamat%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kamat%20SS&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ASiddhesh%2BS%2BKamat%2B) * [ORCID record for Siddhesh S Kamat](http://orcid.org/0000-0001-6132-7574 "Open in new tab") * For correspondence: siddhesh@iiserpune.ac.in * [Abstract](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5802718/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5802718/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5802718/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5802718/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5802718/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Cholesteryl esters (CEs) are widely regarded as inert storage forms of cholesterol, yet their potential to directly engage cellular proteins remains largely unexplored. Here, we establish an integrated chemical proteomic platform to systematically define CE-protein interactions in mammalian cells. We developed and comparatively deployed three orthogonal photoaffinity labeling strategies: (i) metabolic assembly of a bifunctional CE probe through endogenous acyl-CoA:cholesterol acyltransferase activity, (ii) direct delivery of a structurally defined diazirine-alkyne CE analog, and (iii) fragment-assisted subtraction using sterol and fatty acyl control probes to resolve interactions dependent on the intact esterified scaffold. Each probe system was rigorously validated by lipidomics and UV-dependent crosslinking prior to quantitative proteomic analysis. Integration of these complementary modalities identified 495 CE-associated proteins spanning enzymes, transporters, scaffolding proteins, and canonical sterol-binding families. The limited overlap across strategies reveals that lipid-protein engagement is strongly conditioned by biosynthetic origin, probe topology, and intracellular routing. Functional and database annotations further demonstrate enrichment of druggable and disease-linked proteins, connecting CE interactions to metabolic, neurological, and cardiovascular pathways. Collectively, this work provides the first systems-level map of CE-protein interactions and establishes a generalizable, multimodal framework for chemically resolving lipid-protein interactomes. ### Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC-ND 4.0 International license](http://creativecommons.org/licenses/by-nc-nd/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. [Donate to openRxiv ](https://www.zeffy.com/en-US/donation-form/donate-to-make-a-difference-10981) [ Back to top](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1?rss=1#page) [ Previous](https://www.biorxiv.org/content/10.64898/2026.09.22.752128v1 "Speciesformer learns conserved cellular states for cross-species generative virtual cell modeling")[Next ](https://www.biorxiv.org/content/10.64898/2026.09.22.753421v1 "Longitudinal transcriptomic analysis reveals adaptive transcript usage remodeling associated with PARP inhibitor resistance") Posted September 23, 2026. [ Download PDF](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/09/23/2026.09.21.753363.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.09.21.753363v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Orthogonal Chemical Proteomic Strategies Reveal the Cholesteryl Ester Interactome in Mammalian Cells Aakash Chandramouli, Kavita Sharma, Adithya Kallattu, Chaitanya Katkar, Manish Deshmukh, Pooja Thakral, Harinath Chakrapani, Siddhesh S Kamat bioRxiv 2026.09.21.753363; doi: https://doi.org/10.64898/2026.09.21.753363 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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