LOTUS

Beyond drug discovery: Breaking the boundaries of natural products information

https://lotus.nprod.net/

Jonathan BISSON, Adriano Rutz, Guido Pauli, Jean-Luc Wolfender, Pierre-Marie Allard

ACS Spring 2022

Expanding Cheminformatics to Industries Adjacent to Small Molecule Drug Discovery

Situation

Formerly at the University of Illinois Chicago

Now at Collaborative Drug Discovery Inc!^[1]

https://www.collaborativedrug.com/

1. (Sometimes strong) Opinions expressed are solely my own and do not express the views or opinions of my current or previous employer.

Who is behind it

Core team

Adriano Rutz, Jonathan Bisson, Pierre-Marie Allard

The first contributors

Maria Sorokina, Jiří Vondrášek, Daniel Mietchen, Egon Willighagen, Roderic Page, Ralf Stephan, Christoph Steinbeck, Jakub Galgonek, James Graham, Guido Pauli, Arnaud Gaudry, Jean-Luc Wolfender

And all the, too many to cite, contributors on Wikidata.

Funding

NIH U41 AT008706 / P50 AT000155 (NCCIH/ODS)
ChemBioSys (Project-ID 239748522, SFB 1127)
Alfred P.Sloan G-2019-11458
Elixir CZ MEYS LM2018131

The world of Natural Products

Taxomomy is painful

Classification

Taxonomy

👉 https://globalnames.org/

Chemistry

👉 https://npclassifier.ucsd.edu/

What is LOTUS ?

Over 750,000 entries added as of today:

250,000+ unique structures
30,000+ organisms
75,000+ references

LOTUS curation ?

LOTUS bot

Arabidopsis example

Beta-sitosterol example

Queries

Original question

"Hey Wikidata, Which organisms are known to contain quercetin ?"

SPARQL translation

SELECT DISTINCT ?parent_taxon ?parent_taxonname ?taxon ?taxonname WHERE {
VALUES ?classes { wd:Q11173 wd:Q59199015 } ?compound wdt:P31 ?classes; wdt:P235 "REFJWTPEDVJJIY-UHFFFAOYSA-N".
?taxon wdt:P171 ?parent_taxon. { ?compound p:P703 ?stmt.
?stmt ps:P703 ?taxon. { ?stmt prov:wasDerivedFrom ?ref.
?ref pr:P248 ?art. ?art wdt:P356 ?art_doi.
} } ?taxon wdt:P225 ?taxonname.
?parent_taxon wdt:P225 ?parent_taxonname.}

👉 https://w.wiki/36a2

Organisms containing quercetin

Structures found in Quercus spp.

👉 https://w.wiki/36Zk

Compounds structurally similar to antibiotics

Sorted by parent taxon.

👉 https://w.wiki/vnU

Finding overlooked sources of chemicals

Which Zephyranthes species lack compounds known from at least two sister species?

Finding sources in the world

Pigments (Layla Michán)

All natural products that are pigments

pigments

Fragrances, aromas

Compounds similar to Eugenol

eugenol

Cosmetics and allergies

Sources of compounds similar to Dehydroabietic acid

👉 https://w.wiki/4yQq

Sachem

Allows us to link Wikidata with PubChem (we will see another integration in a few slides), DrugBank, ChEMBL, ChEBI. It also allows us to do substructure search and similarity searches.