Exploring Drug Safety Through Knowledge Graphs: Protein Kinase Inhibitors as a Case Study

TL;DR

This paper introduces a knowledge graph framework that integrates diverse drug-related data sources to improve drug safety analysis, exemplified through protein kinase inhibitors and supporting pharmacovigilance and hypothesis generation.

Contribution

The study presents a novel, extensible knowledge graph approach that unifies heterogeneous drug safety data sources for enhanced analysis and ADR prediction.

Findings

Successfully applied to 400 protein kinase inhibitors

Identified known and candidate drugs, target communities, and safety profiles

Supports complex pattern recognition and hypothesis generation

Abstract

Adverse Drug Reactions (ADRs) are a leading cause of morbidity and mortality. Existing prediction methods rely mainly on chemical similarity, machine learning on structured databases, or isolated target profiles, but often fail to integrate heterogeneous, partly unstructured evidence effectively. We present a knowledge graph-based framework that unifies diverse sources, drug-target data (ChEMBL), clinical trial literature (PubMed), trial metadata (ClinicalTrials.gov), and post-marketing safety reports (FAERS) into a single evidence-weighted bipartite network of drugs and medical conditions. Applied to 400 protein kinase inhibitors, the resulting network enables contextual comparison of efficacy (HR, PFS, OS), phenotypic and target similarity, and ADR prediction via target-to-adverse-event correlations. A non-small cell lung cancer case study correctly highlights established and candidate drugs, target communities (ERbB, ALK, VEGF), and tolerability differences. Designed as an orthogonal, extensible analysis and search tool rather than a replacement for current models, the framework excels at revealing complex patterns, supporting hypothesis generation, and enhancing pharmacovigilance. Code and data are publicly available at https://github.com/davidjackson99/PKI_KG.