mims-harvard/tooluniverse-natural-product-dereplication

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.

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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 | | PubChem_get_CID_by_compound_name | name | {IdentifierList:{CID:[...]}} | | PubChem_get_compound_properties_by_CID | cid, properties (e.g. ["MolecularFormula","MolecularWeight","InChIKey","IUPACName"]) | property table — use to obtain an InChIKey for arbitrary compounds |

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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).

# Exact, structure-level
hits = tu.tools.NPAtlas_search_compounds(inchikey="HKSZLNNOFSGOKW-FYTWVXJKSA-N", limit=5)
# MS-feature style (formula or exact mass) — expect multiple isomeric hits
hits = tu.tools.NPAtlas_search_compounds(formula="C28H26N4O3", limit=10)

For each candidate NPAID, fetch the full record to get the producing organism and reference (search results carry origin_organism: null):

rec = tu.tools.NPAtlas_get_compound(npaid="NPA014588")["data"]
organism   = rec["origin_organism"]["name"]            # e.g. "Streptomyces"
lineage    = rec["origin_organism"]["ancestors"]       # domain→...→family
reference  = rec["origin_reference"]                    # title, doi, journal, year

Phase 3 — Assign ChemOnt chemical class

cf = tu.tools.ClassyFire_classify_by_inchikey(inchikey=inchikey)["data"]
# cf["kingdom"], cf["superclass"], cf["class"], cf["subclass"], cf["direct_parent"]
# cf["molecular_framework"], cf["substituents"]

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:

1. Dereplication call — Known microbial NP (with NPAID) or No NPAtlas match (possibly novel / non-microbial).
2. Provenance — producing organism + taxonomic lineage + literature reference (title, DOI, year).
3. Chemical class — ChemOnt kingdom → superclass → class → subclass → direct_parent (+ molecular framework).
4. Identity cross-refs — PubChem CID/IUPAC, InChIKey, formula, exact mass.
5. Interpretation note (see below).

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Interpretation Guidance (dereplication logic)

• 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.

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Worked Example — Staurosporine (trivial name in)

Input: staurosporine (a trivial name).

1. OPSIN name=staurosporine → parsed:false (not systematic IUPAC) → fall through to PubChem.
2. PubChem name→CID = 44259; properties → MolecularFormula C28H26N4O3, MW 466.5, InChIKey HKSZLNNOFSGOKW-FYTWVXJKSA-N.
3. NPAtlas inchikey=HKSZLNNOFSGOKW-FYTWVXJKSA-N → 1 exact hit: NPA014588 Staurosporine, exact_mass 466.2005. → Known microbial NP.
4. NPAtlas get_compound NPA014588 → producing organism Streptomyces (genus; lineage Bacteria → Actinobacteria → Actinobacteria → Streptomycetales → Streptomycetaceae); reference "X-Ray crystal structure of staurosporine: a new alkaloid from a Streptomyces…", DOI 10.1039/C39780000800, 1978.
5. ClassyFire inchikey=HKSZLNNOFSGOKW-FYTWVXJKSA-N → Organic compounds → Organoheterocyclic compounds → Indoles and derivatives → Carbazoles → direct parent Indolocarbazoles; molecular framework: aromatic heteropolycyclic.

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)

Input IUPAC 2-acetyloxybenzoic acid.

1. OPSIN → parsed:true, InChIKey BSYNRYMUTXBXSQ-UHFFFAOYSA-N.
2. NPAtlas inchikey=BSYNRYMUTXBXSQ-... → no microbial NP record ⇒ not a known microbial natural product (it is a semisynthetic drug — consistent with NPAtlas scope).
3. 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.

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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.

Out of Scope → route elsewhere

• General drug/compound identity & ADMET, properties, bioassays → tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery.
• Metabolomics pathway/enrichment analysis → tooluniverse-metabolomics skills.

Completeness Checklist

• [ ] Input type classified (name / formula / mass / InChIKey / SMILES).
• [ ] An InChIKey was obtained (OPSIN or PubChem) when starting from a name/SMILES.
• [ ] NPAtlas searched with the most specific key available; full record fetched for any hit (organism + reference).
• [ ] Known/novel call made with the correct caveats (microbial-only scope).
• [ ] ChemOnt class reported from ClassyFire, or marked unavailable if classified:false.
• [ ] Identity cross-referenced in PubChem (CID/formula/InChIKey agree).
• [ ] Interpretation note included (InChIKey vs formula vs name match; meaning of no-hit / classified:false).
• [ ] Limitations stated; every NPAID, organism, DOI, and class came from a live tool call.