- Drug Repurposing with ToolUniverse
- Systematically identify and evaluate drug repurposing candidates using multiple computational strategies.
- IMPORTANT
-
- Always use English terms in tool calls. Respond in the user's language.
- Core Strategies
- Target-Based
-
- Disease targets -> Find drugs that modulate those targets
- Compound-Based
-
- Approved drugs -> Find new disease indications
- Disease-Driven
- Disease -> Targets -> Match to existing drugs Workflow Overview Phase 1: Disease & Target Analysis Get disease info (OpenTargets), find associated targets, get target details Phase 2: Drug Discovery Search DrugBank, DGIdb, ChEMBL for drugs targeting disease-associated genes Get drug details, indications, pharmacology Phase 3: Safety & Feasibility Assessment FDA warnings, FAERS adverse events, drug interactions, ADMET predictions Phase 4: Literature Evidence PubMed, Europe PMC, clinical trials for existing evidence Phase 5: Scoring & Ranking Composite score: target association + safety + literature + drug properties See: PROCEDURES.md for detailed step-by-step procedures and code patterns. Quick Start from tooluniverse import ToolUniverse tu = ToolUniverse ( use_cache = True ) tu . load_tools ( )
Step 1: Get disease targets
disease_info
tu . tools . OpenTargets_get_disease_id_description_by_name ( diseaseName = "rheumatoid arthritis" ) targets = tu . tools . OpenTargets_get_associated_targets_by_disease_efoId ( efoId = disease_info [ 'data' ] [ 'id' ] , limit = 10 )
Step 2: Find drugs for each target
- for
- target
- in
- targets
- [
- 'data'
- ]
- [
- :
- 5
- ]
- :
- drugs
- =
- tu
- .
- tools
- .
- DGIdb_get_drug_gene_interactions
- (
- gene_name
- =
- target
- [
- 'gene_symbol'
- ]
- )
- Key ToolUniverse Tools
- Disease & Target
- :
- OpenTargets_get_disease_id_description_by_name
- - Disease lookup
- OpenTargets_get_associated_targets_by_disease_efoId
- - Disease targets
- UniProt_get_entry_by_accession
- - Protein details
- Drug Discovery
- :
- drugbank_get_drug_name_and_description_by_target_name
- - Drugs by target
- drugbank_get_drug_name_and_description_by_indication
- - Drugs by indication
- DGIdb_get_drug_gene_interactions
- - Drug-gene interactions
- ChEMBL_search_drugs
- /
- ChEMBL_get_drug_mechanisms
- - Drug search and MOA
- Drug Information
- :
- drugbank_get_drug_basic_info_by_drug_name_or_id
- - Basic info
- drugbank_get_indications_by_drug_name_or_drugbank_id
- - Approved indications
- drugbank_get_pharmacology_by_drug_name_or_drugbank_id
- - Pharmacology
- drugbank_get_targets_by_drug_name_or_drugbank_id
- - Drug targets
- Safety
- :
- FDA_get_warnings_and_cautions_by_drug_name
- - FDA warnings
- FAERS_search_reports_by_drug_and_reaction
- - Adverse events
- FAERS_count_death_related_by_drug
- - Serious outcomes
- drugbank_get_drug_interactions_by_drug_name_or_id
- - Interactions
- Property Prediction
- :
- ADMETAI_predict_admet
- /
- ADMETAI_predict_toxicity
- - ADMET and toxicity
- Literature
- :
- PubMed_search_articles
- /
- EuropePMC_search_articles
- /
- ClinicalTrials_search
- Scoring Criteria
- Category
- Points
- Breakdown
- Target Association
- 0-40
- Strong genetic: 40, Moderate: 25, Pathway-level: 15, Weak: 5
- Safety Profile
- 0-30
- FDA approved: 20, Phase III: 15, Phase II: 10, No black box: +10
- Literature Evidence
- 0-20
- Clinical trials: 5 each (max 15), Preclinical: 1 each (max 10)
- Drug Properties
- 0-10
- High bioavailability: 5, BBB penetration (CNS): 5, Low toxicity: 5
- Best Practices
- Start broad
-
- Query multiple databases (DrugBank, ChEMBL, DGIdb)
- Validate targets
-
- Confirm target-disease associations in OpenTargets
- Safety first
-
- Prioritize approved drugs with known safety profiles
- Literature mining
-
- Search for existing clinical/preclinical evidence
- Consider mechanism
-
- Evaluate biological plausibility
- Batch operations
- Use tu.run_batch() for parallel queries Troubleshooting Problem Solution Disease not found Try synonyms or EFO ID lookup No drugs for target Check HUGO nomenclature, expand to pathway-level, try similar targets Insufficient literature Search drug class instead, check preclinical/animal studies Safety data unavailable Drug may not be US-approved, check EMA or clinical trial safety Reference Files REFERENCE.md - Detailed reference documentation EXAMPLES.md - Sample repurposing analyses PROCEDURES.md - Step-by-step procedures with code REPORT_TEMPLATE.md - Output report template