# The "double-edged sword" effect of non-steroidal anti-inflammatory drugs (NSAIDs) in the treatment of endometriosis (EMS)

## TL;DR

This study shows that NSAIDs used for endometriosis pain may worsen the disease in some cases, but indomethacin has a unique dual effect that could guide more precise treatment.

## Contribution

This study introduces a new framework combining network toxicology, genetic analysis, and structural biology to reveal the 'target-oriented heterogeneous effects' of NSAIDs in endometriosis.

## Key findings

- NSAIDs may promote endometriosis progression via the EPHB4 pathway, but indomethacin uniquely targets both protective and risk-associated pathways.
- Molecular docking confirms indomethacin's strong binding to PTGER4 and EPHB4, explaining its dual regulatory mechanism.
- EPHB4 is identified as a central gene linking NSAID effects to angiogenesis in endometriosis.

## Abstract

Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to alleviate pain associated with endometriosis (EMS), yet the impact of their long-term use on disease progression remains unclear. This study investigates the dual role of NSAIDs in EMS pathogenesis using network toxicology and Mendelian randomization (MR).

The toxicity and ADMET profiles of nine NSAIDs were screened using ProTox 3.0 and ADMETlab 2.0. Potential drug targets were predicted using PharmMapper, STITCH, and SwissTargetPrediction, while EMS-related targets were retrieved from GeneCards, OMIM, and CTD databases. For the MR analysis, cis-eQTLs for whole blood tissue from GTEx v8 served as instrumental variables, based on the inflammatory nature of endometriosis. Outcome data were from an independent GWAS summary dataset (19,588 cases, 213,669 controls). Our analysis adhered to MR independence assumptions, ensuring no sample overlap between exposure and outcome data. Functional enrichment and molecular docking explored the underlying mechanisms.

By integrating drug targets with disease genes, we first identified 463 overlapping targets. We revealed that EPHB4 is a core hub mediating the potential “risk-promoting” effects of nearly all NSAIDs, with its functions enriched in key pathological processes such as angiogenesis. Molecular docking confirmed that eight NSAIDs could stably bind to EPHB4. Crucially, we found that indomethacin exhibited a unique “dual-regulatory” pattern: it simultaneously targeted the protective target PTGER4 and the risk-associated target EPHB4. Molecular docking further substantiated, at the atomic level, that indomethacin possesses strong binding affinity for both targets, providing a structural biology explanation for its observed genetic effects.

This study provides, for the first time, robust causal evidence from both genetic and structural biology perspectives for the “double-edged sword” attribute of NSAIDs in EMS, and proposes a new paradigm of “target-oriented heterogeneous effects.” We found that specific NSAIDs might inadvertently promote disease progression by activating the EPHB4 pathway, while indomethacin stands out as a key exception due to its unique dual-action mechanism. These findings not only offer a critical explanation for the current clinical controversy but also lay a solid scientific foundation for advancing EMS management from “empirical medication” towards “precision-based selection guided by molecular mechanisms.”

The online version contains supplementary material available at 10.1186/s12958-025-01508-7.

Proposing a New Paradigm: By constructing a multi-dimensional analytical framework that integrates network toxicology, causal inference, and structural biology, this study is the first to reveal the “target-oriented heterogeneous effects” of NSAIDs in the treatment of dysmenorrhea caused by endometriosis, challenging the traditional “one-size-fits-all” treatment model.Identifying Key Targets: This study established a complete evidence chain from “target screening” to “causal inference” and finally to “structural validation,” identifying for the first time EPHB4 as the central hub gene mediating the potential risk effects of NSAIDs and elucidating that its function is primarily achieved through angiogenesis pathways.Elucidating a Complex Mechanism: Through cross-validation between genetic causality and molecular structural simulation, we elucidated the unique “dual regulation” mode of indomethacin: mediating a protective effect via PTGER4 while simultaneously mediating a potential risk via EPHB4.Providing Structural Evidence: Molecular docking simulations provided structural biology evidence at the atomic level for the aforementioned genetic effects, confirming that indomethacin possesses high-affinity binding potential with both PTGER4 and EPHB4.Guiding Precision Medication: This study provides a computationally driven, critical basis for the precision medication of endometriosis. It not only offers theoretical support for considering indomethacin as a preferred option but also points the way for the development of novel NSAIDs that avoid the EPHB4 pathway.

Proposing a New Paradigm: By constructing a multi-dimensional analytical framework that integrates network toxicology, causal inference, and structural biology, this study is the first to reveal the “target-oriented heterogeneous effects” of NSAIDs in the treatment of dysmenorrhea caused by endometriosis, challenging the traditional “one-size-fits-all” treatment model.

Identifying Key Targets: This study established a complete evidence chain from “target screening” to “causal inference” and finally to “structural validation,” identifying for the first time EPHB4 as the central hub gene mediating the potential risk effects of NSAIDs and elucidating that its function is primarily achieved through angiogenesis pathways.

Elucidating a Complex Mechanism: Through cross-validation between genetic causality and molecular structural simulation, we elucidated the unique “dual regulation” mode of indomethacin: mediating a protective effect via PTGER4 while simultaneously mediating a potential risk via EPHB4.

Providing Structural Evidence: Molecular docking simulations provided structural biology evidence at the atomic level for the aforementioned genetic effects, confirming that indomethacin possesses high-affinity binding potential with both PTGER4 and EPHB4.

Guiding Precision Medication: This study provides a computationally driven, critical basis for the precision medication of endometriosis. It not only offers theoretical support for considering indomethacin as a preferred option but also points the way for the development of novel NSAIDs that avoid the EPHB4 pathway.

The online version contains supplementary material available at 10.1186/s12958-025-01508-7.