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Drug Discovery
약 발견 작업 흐름에 대한 제약 연구 조수. ChEMBL에 대한 생체 활성 화합물을 검색, 약물과 같은 계산 (Lipinski Ro5, QED, TPSA, 합성 접근성), OpenFDA를 통해 약물 드루그 상호 작용을보고, ADMET 프로파일을 해석하고, 리드 최적화를 지원합니다. 약용 화학 질문, 분자 특성 분석, 임상 pharmacology 및 개방 과학 약 연구에 사용됩니다.
기술 메타데이터
| 소스 | 선택 사항 - hermes skills install official/research/drug-discovery로 설치 |
| 경로 | optional-skills/research/drug-discovery |
| 버전 | 1.0.0 |
| 저자 | bennytimz |
| 라이선스 | MIT |
| 플랫폼 | linux, macos, windows |
| 태그 | science, chemistry, pharmacology, research, health |
참고: 전체 SKILL.md
정보
아래는 Hermes가 이 스킬을 활성화할 때 로드하는 원문 SKILL.md 정의입니다. 명령어, 코드, 식별자를 정확히 보존하기 위해 이 참조 블록은 원문을 유지합니다.
# 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.
```bash
# Search compounds by target name (e.g. "EGFR", "COX-2", "ACE")
TARGET="$1"
ENCODED=$(python3 -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" \
| python3 -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()
"
```
```bash
# 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" \
| python3 -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')}\")
"
```
```bash
# 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" \
| python3 -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')} Ų\")
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.
```bash
COMPOUND="$1"
ENCODED=$(python3 -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" \
| python3 -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} Ų {\"✓\" 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)
```bash
DRUG="$1"
ENCODED=$(python3 -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" \
| python3 -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()
"
```
```bash
DRUG="$1"
ENCODED=$(python3 -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" \
| python3 -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
```bash
COMPOUND="$1"
ENCODED=$(python3 -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" \
| python3 -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)
```bash
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 } } } } } } } }\"}" \
| python3 -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:
1. **State raw values first** — MW, LogP, HBD, HBA, TPSA, RotBonds
2. **Apply rule sets** — Ro5 (Lipinski), Veber, Ghose filter where relevant
3. **Flag liabilities** — metabolic hotspots, hERG risk, high TPSA for CNS penetration
4. **Suggest optimizations** — bioisosteric replacements, prodrug strategies, ring truncation
5. **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` |