Pharmacology API Skills

Query pharmacology databases directly via curl. These endpoints complement the Life Sciences MCPs.

Quick Reference

Task	API	Endpoint
Search compounds	ChEMBL	/molecule/search
Drug mechanism	ChEMBL	/mechanism
Drug indications	ChEMBL	/drug_indication
Bioactivity data	ChEMBL	/activity
Compound properties	PubChem	/compound/name/{name}/property
Ligand-target	IUPHAR	/interactions

Curl Examples

ChEMBL: Compound Search & Details

# Search compound by name
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/search?q=venetoclax&format=json" \
  | jq '.molecules[:1][] | {chembl_id: .molecule_chembl_id, name: .pref_name, max_phase: .max_phase}'

# Get compound by ChEMBL ID
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL3137309?format=json" \
  | jq '{id: .molecule_chembl_id, name: .pref_name, formula: .molecule_properties.full_molformula, mw: .molecule_properties.full_mwt}'

# Get SMILES structure
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL3137309?format=json" \
  | jq '.molecule_structures.canonical_smiles'

ChEMBL: Drug Mechanisms (Critical for Graph Edges!)

# Get mechanism for drug (Drug → Target edge)
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism?molecule_chembl_id=CHEMBL3137309&format=json" \
  | jq '.mechanisms[] | {action: .action_type, mechanism: .mechanism_of_action, target_id: .target_chembl_id}'

# Reverse: Find all drugs for target (Target → Drugs edge)
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism?target_chembl_id=CHEMBL4860&format=json" \
  | jq '.mechanisms[] | {drug_id: .molecule_chembl_id, action: .action_type, mechanism: .mechanism_of_action}'

ChEMBL: Drug Indications

# Get indications for drug (Drug → Disease edge)
curl -s "https://www.ebi.ac.uk/chembl/api/data/drug_indication?molecule_chembl_id=CHEMBL3137309&format=json" \
  | jq '.drug_indications[:5][] | {disease: .mesh_heading, efo: .efo_term, phase: .max_phase_for_ind}'

ChEMBL: Bioactivity Data (Potency Metrics)

# Get activity data (IC50, Ki, EC50)
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity?molecule_chembl_id=CHEMBL3137309&format=json&limit=10" \
  | jq '.activities[] | {target: .target_pref_name, type: .standard_type, value: .standard_value, units: .standard_units}'

# Filter by activity type
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity?molecule_chembl_id=CHEMBL3137309&standard_type=Ki&format=json" \
  | jq '.activities[] | {target: .target_pref_name, Ki: .standard_value, units: .standard_units}'

# Get activities for target
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity?target_chembl_id=CHEMBL4860&format=json&limit=10" \
  | jq '.activities[] | {compound: .molecule_chembl_id, type: .standard_type, value: .standard_value}'

ChEMBL: Structure Search

# Similarity search (find analogs)
SMILES="CC1=CC=CC=C1"  # Example SMILES
curl -s "https://www.ebi.ac.uk/chembl/api/data/similarity/$SMILES/70?format=json" \
  | jq '.molecules[:3][] | {id: .molecule_chembl_id, name: .pref_name, similarity: .similarity}'

# Substructure search
curl -s "https://www.ebi.ac.uk/chembl/api/data/substructure/$SMILES?format=json&limit=5" \
  | jq '.molecules[] | {id: .molecule_chembl_id, name: .pref_name}'

ChEMBL: Target Information

# Get target details
curl -s "https://www.ebi.ac.uk/chembl/api/data/target/CHEMBL4860?format=json" \
  | jq '{id: .target_chembl_id, name: .pref_name, type: .target_type, organism: .organism}'

# Search targets by gene
curl -s "https://www.ebi.ac.uk/chembl/api/data/target/search?q=BCL2&format=json" \
  | jq '.targets[:3][] | {id: .target_chembl_id, name: .pref_name, type: .target_type}'

PubChem: Compound Data

# Get compound by name
curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/JSON" \
  | jq '.PC_Compounds[0] | {cid: .id.id.cid}'

# Get properties
curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/property/MolecularFormula,MolecularWeight,IUPACName/JSON" \
  | jq '.PropertyTable.Properties[0]'

# Get by CID
curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/MolecularFormula,CanonicalSMILES/JSON" \
  | jq '.PropertyTable.Properties[0]'

# Cross-references
curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/xrefs/RegistryID/JSON" \
  | jq '.InformationList.Information[0].RegistryID[:5]'

IUPHAR/GtoPdb: Pharmacology

# Search ligands (drugs/compounds)
curl -s "https://www.guidetopharmacology.org/services/ligands?name=ibuprofen" \
  | jq '.[:1][] | {id: .ligandId, name, type, approved}'

# Get ligand details
curl -s "https://www.guidetopharmacology.org/services/ligands/2713" \
  | jq '{id: .ligandId, name, type, approved, synonyms}'

# Search targets
curl -s "https://www.guidetopharmacology.org/services/targets?name=dopamine" \
  | jq '.[:3][] | {id: .targetId, name, type: .type}'

# Get target-ligand interactions
curl -s "https://www.guidetopharmacology.org/services/ligands/2713/interactions" \
  | jq '.[:3][] | {target: .targetName, action: .action, affinity}'

DrugBank: Drug Data (API Key Required)

# Search drugs (commercial API)
curl -s "https://api.drugbank.com/v1/drugs?q=venetoclax" \
  -H "Authorization: Bearer YOUR_API_KEY" \
  | jq '.[:1][] | {drugbank_id, name, description}'

Common Workflow: Drug Repurposing

# 1. Find target for known drug
TARGET=$(curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism?molecule_chembl_id=CHEMBL3137309&format=json" \
  | jq -r '.mechanisms[0].target_chembl_id')

# 2. Find other drugs for same target
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism?target_chembl_id=$TARGET&format=json" \
  | jq '.mechanisms[] | {drug: .molecule_chembl_id, mechanism: .mechanism_of_action}'

# 3. Get indications for alternative drug
curl -s "https://www.ebi.ac.uk/chembl/api/data/drug_indication?molecule_chembl_id=CHEMBL2107358&format=json" \
  | jq '.drug_indications[:3][] | {disease: .mesh_heading, phase: .max_phase_for_ind}'

Rate Limits

API	Limit	Auth Required
ChEMBL	100 req/s	No
PubChem	5 req/s	No
DrugBank	Varies	Yes (commercial)
IUPHAR	10 req/s	No

Query Best Practices

Drug Discovery vs Repurposing

• Drug repurposing: Use max_phase≥2 filter (want clinical validation, shorter approval path)
• General discovery: No phase filter (include preclinical tools, mechanism probes, research reagents)
• Target validation: No phase filter needed for mechanism studies

Query Efficiency

• Check mechanisms (/mechanism endpoint) before bioactivity data
• Use target_chembl_id for reverse lookups (find drugs for target)
• Limit activity queries with &limit=10 for exploration

Common Pitfalls

• Don't filter by phase for mechanism discovery
• Don't assume approved drugs are the only useful compounds
• Preclinical tool compounds often have better selectivity data

See Also

• references/chembl-resources.md - ChEMBL resource endpoints
• references/pubchem-pug.md - PubChem PUG REST syntax