tooluniverse-drug-repurposing - Claude MCP Skill

# 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

1. **Target-Based**: Disease targets -> Find drugs that modulate those targets
2. **Compound-Based**: Approved drugs -> Find new disease indications
3. **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

```python
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

1. **Start broad**: Query multiple databases (DrugBank, ChEMBL, DGIdb)
2. **Validate targets**: Confirm target-disease associations in OpenTargets
3. **Safety first**: Prioritize approved drugs with known safety profiles
4. **Literature mining**: Search for existing clinical/preclinical evidence
5. **Consider mechanism**: Evaluate biological plausibility
6. **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
- Related skills: disease-intelligence-gatherer, chemical-compound-retrieval, tooluniverse-sdk