AI-Driven Drug Repurposing: Network Pharmacology, Biomedical Knowledge Graphs & Predictive Drug Discovery

Aim

Workshop Objectives

Workshop Structure

AI-Driven Drug Repurposing: Network Pharmacology, Biomedical Knowledge Graphs & Predictive Drug Discovery

📅 Day 1 – Network Pharmacology, Drug–Target Interactions & Disease Pathway Analysis

Focus: Identifying therapeutic targets through network pharmacology, molecular interactions, and pathway analysis, using a single disease case study (Major Depressive Disorder) carried through all three days.

• Introduction to AI-driven drug repurposing, network medicine, and landmark repurposing success stories.
• Disease-associated gene identification and target validation using Open Targets.
• Drug–target interaction mapping and bioactivity analysis using ChEMBL.
• Protein–protein interaction (PPI) network construction using STRING, including the effect of confidence thresholds.
• Molecular network visualization, hub-gene identification, and topology analysis using Cytoscape.
• Biological pathway enrichment and functional interpretation using Reactome.
• Integration of disease–gene–drug–pathway evidence for therapeutic target prioritization.

🛠️ Hands-On Lab: Drug–Target Network Construction & Pathway Enrichment
Identify disease genes, map drug–target interactions, construct PPI networks, and analyze enriched pathways.

🧰 Tools Covered: Open Targets | ChEMBL | STRING | Cytoscape | Reactome

📅 Day 2 – Transcriptomic Signatures & Signature-Based Drug Repurposing

Focus: Deriving a disease signature from patient transcriptomic data and identifying drugs that reverse it.

• Introduction to transcriptomics-driven repurposing and the “signature reversal” concept.
• Public omics data sourcing from GEO, dataset selection, and quality control (batch effects, confounders).
• Differential expression analysis using GEO2R and limma.
• Functional enrichment of differentially expressed genes using Enrichr/gseapy.
• Integration of DEGs with Day 1 network genes to refine disease-gene candidates.
• Signature-based drug ranking using CMap/LINCS L1000 (L1000CDS2, SigCom LINCS).
• Common pitfalls: small sample sizes, brain tissue vs. blood, and cross-dataset replication.
• Real research case study: transcriptomic and network-based analysis in major depressive disorder and bipolar disorder.

🛠️ Hands-On Lab: Disease Signature Extraction & Signature-Reversal Drug Ranking
Analyze a GEO dataset to extract DEGs, perform enrichment analysis, and generate a ranked list of signature-reversing drugs.

🧰 Tools Covered: GEO/GEO2R | limma | Enrichr/gseapy | L1000CDS2 | SigCom LINCS | Google Colab

📅 Day 3 – Candidate Prioritization & Evidence Validation

Focus: Evaluating network-derived and signature-derived drug candidates using biological, pharmacological, and clinical evidence.

• Integration of network pharmacology results (Day 1) and signature-reversal predictions (Day 2) into a candidate shortlist.
• Evidence-weighted candidate ranking using a scoring matrix (target score, pathway relevance, reversal score, literature, trials, safety).
• Drug–disease association analysis and mechanism-of-action interpretation.
• Drug-likeness and ADMET profiling using SwissADME, including blood–brain barrier penetration.
• Introduction to molecular docking using SwissDock.
• Preliminary drug safety and adverse-effect assessment using OpenFDA and SIDER.
• Scientific literature verification using PubMed.
• Clinical trial evidence assessment using ClinicalTrials.gov.
• AI-assisted drug repurposing using the Repurpose Drug Discovery Lab.
• Limitations and common mistakes in repurposing studies; IP and regulatory considerations.
• Development of therapeutic hypotheses and experimental validation strategies.

🛠️ Hands-On Lab: Therapeutic Candidate Prioritization & Evidence Validation
Use the Repurpose Drug Discovery Lab at Live-Labs.org to analyze drug–disease associations, evaluate supporting evidence, and prioritize promising therapeutic candidates. Each participant/team presents their top 3 candidates with an evidence table and one validation proposal.

🧰 Tools Covered: Repurpose Drug Discovery Lab | Open Targets | ChEMBL | SwissADME | PubMed | ClinicalTrials.gov

Who Should Enrol?

Important Dates

Workshop Outcomes

Fee Structure