---
title: "KPB82 is a potent, selective ACER2 inhibitor that protects cells from doxorubicin toxicity"
id: "biorxiv-0-kpb82-potently-and-selectively-inhibits-acer2-and-protects-tumor-and-primary"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-0-kpb82-potently-and-selectively-inhibits-acer2-and-protects-tumor-and-primary"
content_type: "clinical_feed_article"
specialty: "Pharmacology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1?rss=1"
published_at: "2026-10-02T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# KPB82 is a potent, selective ACER2 inhibitor that protects cells from doxorubicin toxicity
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-0-kpb82-potently-and-selectively-inhibits-acer2-and-protects-tumor-and-primary
- **Specialty:** [Pharmacology](https://medichelpline.com/clinical-feed/pharmacology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1?rss=1)
- **Published At:** 2026-10-02T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- Alkaline ceramidase 2 (**ACER2**) hydrolyzes ceramides to sphingosine and free fatty acids and influences cell proliferation, survival, and the DNA damage response. - The small molecule N-[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]dodecane-1-sulfonamide (**KPB82**) was identified as a potent, selective inhibitor of **ACER2**. - In vitro enzyme assays reported an IC50 of 190 nM for **KPB82** against ACER2, with minimal activity against acid and neutral ceramidases (IC50 > 100 µM) and no meaningful inhibition of alkaline ceramidase 1 or 3. - Kinetic analyses indicated that **KPB82** acts as a competitive inhibitor of ACER2. - An AlphaFold3-predicted 3D model of ACER2 revealed Zn2+-coordinating histidines and a substrate-binding pocket used for study of inhibitor binding. - Molecular docking placed **KPB82** in the ACER2 substrate pocket, predicting hydrogen bonds with catalytically important residues Asp93 and His215 and hydrophobic interactions with surrounding residues. - Lactate dehydrogenase (LDH) release assays showed that **KPB82** reduced cytotoxicity in HeLa cells overexpressing ACER2 and in HCT116, RT4, and human umbilical vein endothelial cells (HUVECs) treated with the DNA-damaging agent **doxorubicin**. - Lipidomic analysis demonstrated that **KPB82** inhibited sphingosine production driven by ACER2 overexpression or by doxorubicin treatment. - Collectively, the data support **KPB82** as a selective pharmacological tool to suppress ACER2-dependent biochemical and cellular responses; the work is reported as a preprint and has not been peer reviewed.
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Arpita Devi 1 Stony Brook University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Arpita%2BDevi%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Devi%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AArpita%2BDevi%2B) Ruijuan Xu 1 Stony Brook University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Ruijuan%2BXu%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Xu%20R&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ARuijuan%2BXu%2B) Zdzislaw Szulc 2 Medical University of South Carolina; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Zdzislaw%2BSzulc%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Szulc%20Z&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AZdzislaw%2BSzulc%2B) Ian Kim 1 Stony Brook University; 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* [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Cungui%2BMao%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Mao%20C&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ACungui%2BMao%2B) * [ORCID record for Cungui Mao](http://orcid.org/0000-0002-1330-1887 "Open in new tab") * For correspondence: cungui.mao@stonybrook.edu * [Abstract](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5834001/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5834001/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5834001/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5834001/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5834001/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Alkaline ceramidase 2 (ACER2) catalyzes the hydrolysis of ceramides into sphingosine and free fatty acids, playing crucial roles in regulating various biological processes, including but not limited to cell proliferation, survival, and the DNA damage response. However, a pharmacological tool that regulates its catalytic and signaling functions remains to be developed. In this study, N-[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]dodecane-1-sulfonamide (KPB82) was identified as a potent and selective ACER2 inhibitor. In vitro enzymatic assays showed that KPB82 inhibited ACER2 with an IC50 of 190 nM, while displaying minimal activity against acid and neutral ceramidases (IC50> 100 µM) and no significant inhibition of alkaline ceramidase 1 or alkaline ceramidase 3. Enzymatic kinetic studies revealed that KPB82 is a competitive inhibitor of ACER2. The three-dimensional structure of ACER2 was modeled in the AlphaFold3 server, revealing key Zn2+-coordinating histidine residues and a substrate-binding pocket. Molecular docking studies demonstrated that KPB82 binds ACER2 within this pocket, forming hydrogen bonds with the catalytically important amino residues, Asp93 and His215, and interacting with several hydrophobic residues. Lactate dehydrogenase release assays revealed that KPB82 significantly reduced cytotoxicity in HeLa cells overexpressing ACER2, as well as in HCT116 cells, RT4 cells, and human umbilical vein endothelial cells treated with the DNA-damaging agent doxorubicin. Lipidomic analysis showed that KPB82 inhibited sphingosine production in response to ACER2 overexpression or doxorubicin treatment. Collectively, these findings demonstrate that KPB82 is a potent and selective ACER2 inhibitor capable of suppressing ACER2-dependent biological processes and highlight its potential as a tool for studying ceramide metabolism and ACER2-mediated signaling pathways. ### Competing Interest Statement The authors have declared no competing interest. ## Funder Information Declared National Institutes of Health, https://ror.org/01cwqze88, R01CA273263, P01CA097132 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 4.0 International license](http://creativecommons.org/licenses/by/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. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.09.29.754712v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/10/02/2026.09.29.754712.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/10.64898/2026.09.29.754712v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) KPB82 potently and selectively inhibits ACER2 and protects tumor and primary cells from doxorubicin-induced cytotoxicity Arpita Devi, Ruijuan Xu, Zdzislaw Szulc, Ian Kim, Mohamed Salama, Krishna P Bhabak, Christoph Arenz, Daniel Canals, Yusuf A Hannun, Cungui Mao bioRxiv 2026.09.29.754712; doi: https://doi.org/10.64898/2026.09.29.754712 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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