SMILES Profiling#

Turn one SMILES into a compact pharmacology profile.

Tool stack#

ToolUseSwissTargetPredictionPredicted protein targets with probabilitiesPubChemExact CID, synonyms, MW, XLogP, TPSA, HBD/HBA, rotatable bondsADMETlab 3.0ADMET flags, drug-likeness, toxicity sectionsChEMBLSimilarity hits, max phase, known mechanisms, target namesPK-SmartHuman and animal PK estimates (VDss, CL, t½, fu, MRT)

Workflow#

1. Use the user-provided SMILES as-is unless it clearly needs cleanup.
2. Normalize only obvious salts/counterions.
3. Run SwissTargetPrediction for target hypotheses.
4. Run PubChem for identity and physicochemical baseline.
5. Run ADMETlab 3.0 for ADMET flags and drug-likeness.
6. Run ChEMBL for similarity hits and mechanism context.
7. Run PK-Smart last for PK estimates.
8. Merge the outputs into one short report, preferring direct database evidence over predictions.

Preferred scripts#

• scripts/run_smiles_profile.py <SMILES> for the full report.
• scripts/run_smiles_smoke.py --cases <tsv> for regression/benchmark runs.

Extraction notes#

• SwissTargetPrediction: capture the top 5 targets, probabilities, and species.
• PubChem: capture CID, IUPAC name, synonyms, MW, XLogP, TPSA, HBD/HBA, and rotatable bonds.
• ADMETlab 3.0: capture the section list and any obvious toxicity/drug-likeness flags.
• ChEMBL: capture the similarity threshold, top hits, max phase, mechanism_of_action, and target name.
• PK-Smart: capture VDss, CL, t½, fu, MRT, and animal PK when available.

Handling edge cases#

• Salts/mixtures: strip common counterions first.
• Invalid SMILES: fail cleanly, do not crash.
• Missing tools: continue with the remaining sources.
• PubChem miss: report the miss and continue.
• ChEMBL miss: automatically fall back from 90 → 80 → 70 similarity.

Output shape#

text

SMILES: CC(=O)OC1=CC=CC=C1C(=O)O

## SwissTargetPrediction
- Top target: PTGS1 (prob: 0.76)

## PubChem
- CID: 2244 | Name: 2-acetyloxybenzoic acid
- MW: 180.16 Da | XLogP: 1.2 | TPSA: 63.6 Ų

## ADMETlab 3.0
- MW: 180.04 Da | QED: N/A

## ChEMBL
- Top hit: CHEMBL25 ASPIRIN | sim 100 | phase 4
- Mechanism: Cyclooxygenase inhibitor -> Cyclooxygenase

## PK-Smart
- VDss: 0.23 L/kg | CL: 10.41 mL/min/kg
- t½: 0.34 hr | fu: 0.67