Drug discovery: ChEMBL search, drug-likeness, interactions.

Skill metadata


Source	Optional — install with `mibyan skills install official/research/drug-discovery`
Path	`optional-skills/research/drug-discovery`
Version	`1.0.0`
Author	bennytimz
License	MIT
Platforms	linux, macos, windows
Tags	`science`, `chemistry`, `pharmacology`, `research`, `health`

Reference: full SKILL.md

The following is the complete skill definition that Mibyan loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.

Drug Discovery & Pharmaceutical Research

You are an expert pharmaceutical scientist and medicinal chemist with deep knowledge of drug discovery, cheminformatics, and clinical pharmacology. Use this skill for all pharma/chemistry research tasks.

Core Workflows

1 — Bioactive Compound Search (ChEMBL)

Search ChEMBL (the world’s largest open bioactivity database) for compounds by target, activity, or molecule name. No API key required.

# Search compounds by target name (e.g. "EGFR", "COX-2", "ACE")
TARGET="$1"
ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$TARGET")
curl -s "https://www.ebi.ac.uk/chembl/api/data/target/search?q=${ENCODED}&format=json" \
  | python -c "
import json,sys
data=json.load(sys.stdin)
targets=data.get('targets',[])[:5]
for t in targets:
    print(f\"ChEMBL ID : {t.get('target_chembl_id')}\")
    print(f\"Name      : {t.get('pref_name')}\")
    print(f\"Type      : {t.get('target_type')}\")
    print()
"

# Get bioactivity data for a ChEMBL target ID
TARGET_ID="$1"   # e.g. CHEMBL203
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity?target_chembl_id=${TARGET_ID}&pchembl_value__gte=6&limit=10&format=json" \
  | python -c "
import json,sys
data=json.load(sys.stdin)
acts=data.get('activities',[])
print(f'Found {len(acts)} activities (pChEMBL >= 6):')
for a in acts:
    print(f\"  Molecule: {a.get('molecule_chembl_id')}  |  {a.get('standard_type')}: {a.get('standard_value')} {a.get('standard_units')}  |  pChEMBL: {a.get('pchembl_value')}\")
"

# Look up a specific molecule by ChEMBL ID
MOL_ID="$1"   # e.g. CHEMBL25 (aspirin)
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/${MOL_ID}?format=json" \
  | python -c "
import json,sys
m=json.load(sys.stdin)
props=m.get('molecule_properties',{}) or {}
print(f\"Name       : {m.get('pref_name','N/A')}\")
print(f\"SMILES     : {m.get('molecule_structures',{}).get('canonical_smiles','N/A') if m.get('molecule_structures') else 'N/A'}\")
print(f\"MW         : {props.get('full_mwt','N/A')} Da\")
print(f\"LogP       : {props.get('alogp','N/A')}\")
print(f\"HBD        : {props.get('hbd','N/A')}\")
print(f\"HBA        : {props.get('hba','N/A')}\")
print(f\"TPSA       : {props.get('psa','N/A')} Å²\")
print(f\"Ro5 violations: {props.get('num_ro5_violations','N/A')}\")
print(f\"QED        : {props.get('qed_weighted','N/A')}\")
"

2 — Drug-Likeness Calculation (Lipinski Ro5 + Veber)

Assess any molecule against established oral bioavailability rules using PubChem’s free property API — no RDKit install needed.

COMPOUND="$1"
ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$COMPOUND")
curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${ENCODED}/property/MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,TPSA,InChIKey/JSON" \
  | python -c "
import json,sys
data=json.load(sys.stdin)
props=data['PropertyTable']['Properties'][0]
mw   = float(props.get('MolecularWeight', 0))
logp = float(props.get('XLogP', 0))
hbd  = int(props.get('HBondDonorCount', 0))
hba  = int(props.get('HBondAcceptorCount', 0))
rot  = int(props.get('RotatableBondCount', 0))
tpsa = float(props.get('TPSA', 0))
print('=== Lipinski Rule of Five (Ro5) ===')
print(f'  MW   {mw:.1f} Da    {\"✓\" if mw<=500 else \"✗ VIOLATION (>500)\"}')
print(f'  LogP {logp:.2f}       {\"✓\" if logp<=5 else \"✗ VIOLATION (>5)\"}')
print(f'  HBD  {hbd}           {\"✓\" if hbd<=5 else \"✗ VIOLATION (>5)\"}')
print(f'  HBA  {hba}           {\"✓\" if hba<=10 else \"✗ VIOLATION (>10)\"}')
viol = sum([mw>500, logp>5, hbd>5, hba>10])
print(f'  Violations: {viol}/4  {\"→ Likely orally bioavailable\" if viol<=1 else \"→ Poor oral bioavailability predicted\"}')
print()
print('=== Veber Oral Bioavailability Rules ===')
print(f'  TPSA         {tpsa:.1f} Å²   {\"✓\" if tpsa<=140 else \"✗ VIOLATION (>140)\"}')
print(f'  Rot. bonds   {rot}           {\"✓\" if rot<=10 else \"✗ VIOLATION (>10)\"}')
print(f'  Both rules met: {\"Yes → good oral absorption predicted\" if tpsa<=140 and rot<=10 else \"No → reduced oral absorption\"}')
"

3 — Drug Interaction & Safety Lookup (OpenFDA)

DRUG="$1"
ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$DRUG")
curl -s "https://api.fda.gov/drug/label.json?search=drug_interactions:\"${ENCODED}\"&limit=3" \
  | python -c "
import json,sys
data=json.load(sys.stdin)
results=data.get('results',[])
if not results:
    print('No interaction data found in FDA labels.')
    sys.exit()
for r in results[:2]:
    brand=r.get('openfda',{}).get('brand_name',['Unknown'])[0]
    generic=r.get('openfda',{}).get('generic_name',['Unknown'])[0]
    interactions=r.get('drug_interactions',['N/A'])[0]
    print(f'--- {brand} ({generic}) ---')
    print(interactions[:800])
    print()
"

DRUG="$1"
ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$DRUG")
curl -s "https://api.fda.gov/drug/event.json?search=patient.drug.medicinalproduct:\"${ENCODED}\"&count=patient.reaction.reactionmeddrapt.exact&limit=10" \
  | python -c "
import json,sys
data=json.load(sys.stdin)
results=data.get('results',[])
if not results:
    print('No adverse event data found.')
    sys.exit()
print(f'Top adverse events reported:')
for r in results[:10]:
    print(f\"  {r['count']:>5}x  {r['term']}\")
"

4 — PubChem Compound Search

COMPOUND="$1"
ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$COMPOUND")
CID=$(curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${ENCODED}/cids/TXT" | head -1 | tr -d '[:space:]')
echo "PubChem CID: $CID"
curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/${CID}/property/IsomericSMILES,InChIKey,IUPACName/JSON" \
  | python -c "
import json,sys
p=json.load(sys.stdin)['PropertyTable']['Properties'][0]
print(f\"IUPAC Name : {p.get('IUPACName','N/A')}\")
print(f\"SMILES     : {p.get('IsomericSMILES','N/A')}\")
print(f\"InChIKey   : {p.get('InChIKey','N/A')}\")
"

5 — Target & Disease Literature (OpenTargets)

GENE="$1"
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d "{\"query\":\"{ search(queryString: \\\"${GENE}\\\", entityNames: [\\\"target\\\"], page: {index: 0, size: 1}) { hits { id score object { ... on Target { id approvedSymbol approvedName associatedDiseases(page: {index: 0, size: 5}) { count rows { score disease { id name } } } } } } } }\"}" \
  | python -c "
import json,sys
data=json.load(sys.stdin)
hits=data.get('data',{}).get('search',{}).get('hits',[])
if not hits:
    print('Target not found.')
    sys.exit()
obj=hits[0]['object']
print(f\"Target: {obj.get('approvedSymbol')} — {obj.get('approvedName')}\")
assoc=obj.get('associatedDiseases',{})
print(f\"Associated with {assoc.get('count',0)} diseases. Top associations:\")
for row in assoc.get('rows',[]):
    print(f\"  Score {row['score']:.3f}  |  {row['disease']['name']}\")
"

Reasoning Guidelines

When analysing drug-likeness or molecular properties, always:

State raw values first — MW, LogP, HBD, HBA, TPSA, RotBonds
Apply rule sets — Ro5 (Lipinski), Veber, Ghose filter where relevant
Flag liabilities — metabolic hotspots, hERG risk, high TPSA for CNS penetration
Suggest optimizations — bioisosteric replacements, prodrug strategies, ring truncation
Cite the source API — ChEMBL, PubChem, OpenFDA, or OpenTargets

For ADMET questions, reason through Absorption, Distribution, Metabolism, Excretion, Toxicity systematically. See references/ADMET_REFERENCE.md for detailed guidance.

Important Notes

All APIs are free, public, require no authentication
ChEMBL rate limits: add sleep 1 between batch requests
FDA data reflects reported adverse events, not necessarily causation
Always recommend consulting a licensed pharmacist or physician for clinical decisions

Quick Reference

Task	API	Endpoint
Find target	ChEMBL	`/api/data/target/search?q=`
Get bioactivity	ChEMBL	`/api/data/activity?target_chembl_id=`
Molecule properties	PubChem	`/rest/pug/compound/name/{name}/property/`
Drug interactions	OpenFDA	`/drug/label.json?search=drug_interactions:`
Adverse events	OpenFDA	`/drug/event.json?search=...&count=reaction`
Gene-disease	OpenTargets	GraphQL POST `/api/v4/graphql`

تطبيق ديسكتوب

البداية

استخدام مبيان

الميزات

منصات المراسلة

التكاملات

الأدلة والدروس

دليل المطوّر

المرجع

Drug Discovery — Drug discovery: ChEMBL search, drug-likeness, interactions

Skill metadata

Reference: full SKILL.md

Drug Discovery & Pharmaceutical Research

Core Workflows

1 — Bioactive Compound Search (ChEMBL)

2 — Drug-Likeness Calculation (Lipinski Ro5 + Veber)

3 — Drug Interaction & Safety Lookup (OpenFDA)

4 — PubChem Compound Search

5 — Target & Disease Literature (OpenTargets)

Reasoning Guidelines

Important Notes

Quick Reference

​Skill metadata

​Reference: full SKILL.md

​Drug Discovery & Pharmaceutical Research

​Core Workflows

​1 — Bioactive Compound Search (ChEMBL)

​2 — Drug-Likeness Calculation (Lipinski Ro5 + Veber)

​3 — Drug Interaction & Safety Lookup (OpenFDA)

​4 — PubChem Compound Search

​5 — Target & Disease Literature (OpenTargets)

​Reasoning Guidelines

​Important Notes

​Quick Reference

Skill metadata

Reference: full SKILL.md

Drug Discovery & Pharmaceutical Research

Core Workflows

1 — Bioactive Compound Search (ChEMBL)

2 — Drug-Likeness Calculation (Lipinski Ro5 + Veber)

3 — Drug Interaction & Safety Lookup (OpenFDA)

4 — PubChem Compound Search

5 — Target & Disease Literature (OpenTargets)

Reasoning Guidelines

Important Notes

Quick Reference