Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).
Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).
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Natural Product Dereplication & Chemotaxonomy
Decide whether a putative natural product is already known, identify the microbe that produces it, attach the literature reference, and assign its ChemOnt chemical class. This is the dereplication question every NP chemist and metabolomics analyst asks of a new feature: "have we seen this before, and what makes it?"
LOOK UP DON'T GUESS: Never assume an NPAID, producing organism, exact mass, or chemical class. Every identity, provenance, and taxonomy claim must come from a live tool call.
Scope (microbial NPs only): NPAtlas covers natural products from bacteria and fungi. It does NOT cover plant, animal, or marine-invertebrate metabolites unless a microbial producer was reported. A "no NPAtlas hit" therefore means not a known microbial NP — it does not prove the molecule is novel in an absolute sense.
Backing Tools (all keyless; verify before quoting)
Tool
Input
Returns
NPAtlas_search_compounds
name / inchikey / formula / smiles, limit
list of {npaid, name, molecular_formula, molecular_weight, exact_mass, inchikey, smiles}. (origin_organism is null here — fetch the full record for provenance)
NPAtlas_get_compound
npaid (e.g. NPA014588)
full record incl. origin_organism (producing microbe + taxonomic lineage) and origin_reference (title/doi/journal/year)
ClassyFire_classify_by_inchikey
inchikey (full 27-char)
ChemOnt kingdom→superclass→class→subclass→direct_parent, molecular_framework, substituents. classified:false if not in cache
OPSIN_name_to_structure
name (systematic IUPAC)
smiles / inchi / inchikey. parsed:false for trade/trivial names
property table — use to obtain an InChIKey for arbitrary compounds
Workflow
Phase 0: Classify input — name / formula / exact mass / InChIKey / SMILES?
Phase 1: Obtain an InChIKey (the universal key for ClassyFire & precise NPAtlas match)
Phase 2: Dereplicate against NPAtlas (known microbial NP? which organism? which paper?)
Phase 3: Assign ChemOnt chemical class via ClassyFire
Phase 4: Cross-reference identity in PubChem
Phase 5: Report — known/novel call + provenance + class hierarchy + interpretation note
Phase 0 — Classify the input
Full InChIKey (27 chars, XXXXXXXXXXXXXX-XXXXXXXXXX-X) → skip to Phase 2; it is already the universal key.
Molecular formula / exact mass → go straight to NPAtlas formula search (Phase 2); these are the rawest dereplication inputs (typical of an untargeted MS feature).
SMILES → usable directly in NPAtlas_search_compounds(smiles=...); also feed to PubChem for an InChIKey.
Systematic IUPAC name (e.g. 2-acetyloxybenzoic acid) → Phase 1 via OPSIN.
Trivial / trade / common name (e.g. staurosporine, penicillin) → Phase 1 via PubChem (OPSIN will return parsed:false for these).
Phase 1 — Obtain an InChIKey
# Systematic IUPAC name → structure (OPSIN). parsed:false ⇒ fall through to PubChem.
op = tu.tools.OPSIN_name_to_structure(name="2-acetyloxybenzoic acid")
inchikey = op["data"]["inchikey"] # only if op["data"]["parsed"]# Trivial/common name → PubChem CID → properties (incl. InChIKey)
cid = tu.tools.PubChem_get_CID_by_compound_name(name="staurosporine")["data"]["IdentifierList"]["CID"][0]
props = tu.tools.PubChem_get_compound_properties_by_CID(
cid=cid, properties=["MolecularFormula","MolecularWeight","InChIKey","IUPACName"])
inchikey = props["data"]["PropertyTable"]["Properties"][0]["InChIKey"]
The InChIKey is what makes dereplication exact: an InChIKey match is a structure match; a name match is not (synonyms, analogs, and salts share names).
Phase 2 — Dereplicate against NPAtlas
Search by the most specific key available. Prefer InChIKey (exact structure), then formula (catches isomers — useful for an MS feature with only a formula), then name (loosest — returns analogs).
If classified:false, the InChIKey is not in the ClassyFire cache — report the class as unavailable (do not invent one). A correct InChIKey is required; a wrong stereo/protonation layer will miss the cache.
Phase 4 — Cross-reference identity in PubChem
Confirm the same molecule exists in PubChem (CID, IUPAC name, formula, MW) so the identity is anchored to a second independent database. Disagreement in molecular formula between NPAtlas and PubChem is a red flag that the name/structure resolution went astray.
Phase 5 — Report
Deliver:
Dereplication call — Known microbial NP (with NPAID) orNo NPAtlas match (possibly novel / non-microbial).
InChIKey hit in NPAtlas = structure-level match ⇒ confidently a known microbial NP. Quote the NPAID, organism, and paper.
Formula / exact-mass hit(s) only = candidate(s) at the molecular-formula level. Multiple isomers can share one formula and exact mass (e.g. C28H26N4O3, 466.2005 Da, returns both staurosporine and an ardeemin derivative). Treat these as a ranked candidate list, not an identification — confirm with InChIKey, MS/MS, or NMR before claiming identity.
Name hit only = weakest evidence. A name search returns analogs and congeners (searching "staurosporine" returns 5'-hydroxystaurosporine, etc.), not necessarily the exact molecule. Always escalate to an InChIKey check.
No NPAtlas hit = not a known microbial natural product. Possible meanings: genuinely novel; a plant/animal/marine metabolite outside NPAtlas scope; or a synthetic/derivatized compound. State which interpretations remain open — do not declare "novel" unconditionally.
ClassyFire classified:false = ChemOnt has no cached classification for that exact InChIKey (often because the InChIKey's stereo/charge layer differs from the cached entry, or the compound is new). Report class as unavailable rather than guessing.
OPSIN parsed:false = the name was not systematic IUPAC (trade/trivial name); route to PubChem for an InChIKey instead.
Worked Example — Staurosporine (trivial name in)
Input: staurosporine (a trivial name).
OPSINname=staurosporine → parsed:false (not systematic IUPAC) → fall through to PubChem.
Call: Known microbial natural product (NPA014588), an indolocarbazole alkaloid produced by Streptomyces, first reported 1978.
Dereplication-logic footnote: the formula C28H26N4O3 (exact mass 466.2005) alone is not unique — NPAtlas formula search returns 2 isomers (staurosporine and 5-N-acetyl-15b-didehydroardeemin). The InChIKey is what pins the identity to staurosporine specifically. An MS feature with only this formula would need MS/MS or NMR to choose between the isomers.
Worked Example — Acetylsalicylic acid (systematic name in)
NPAtlasinchikey=BSYNRYMUTXBXSQ-... → no microbial NP record ⇒ not a known microbial natural product (it is a semisynthetic drug — consistent with NPAtlas scope).
ClassyFire → Organic compounds → Benzenoids → Benzene and substituted derivatives → Benzoic acids and derivatives → direct parent Acylsalicylic acids.
Call: Classified into ChemOnt (acylsalicylic acid), but no NPAtlas microbial-NP provenance — illustrating a legitimate "no hit" that is not a novel NP.
Limitations (be honest in every report)
NPAtlas = microbial NPs only (bacteria + fungi). No plant, animal, or marine-invertebrate metabolites unless a microbial producer was reported. Absence is not proof of novelty.
ClassyFire is a cache lookup by InChIKey. classified:false means "not cached for this exact InChIKey", not "unclassifiable". Wrong stereo/charge layers miss the cache.
Name search ≠ structure match. NPAtlas/PubChem name searches return synonyms, analogs, and salts. Always confirm identity at the InChIKey level before declaring a compound "known".
Formula/exact-mass hits are candidate lists, not identifications — isomers share formulas. Confirm with orthogonal evidence (MS/MS, NMR, InChIKey).
OPSIN parses systematic IUPAC names only — trivial/trade names return parsed:false; route them through PubChem.
Search-result records carry origin_organism: null; provenance requires the NPAtlas_get_compound full record.
