01 April 2014

Funky fragments

Natural products have led to many approved drugs, and there is an increasing appreciation that Nature often knows best. Indeed, several published fragment libraries incorporate natural products or natural product-like molecules (see for example here, here, and here). With all this attention, it was inevitable that commercial fragment suppliers would spot this market need.

SerpentesOleum, Inc. has just launched a library they call FUNK: Fragments Uncovered in Natural Kompounds. This set consists of several hundred natural products and derived fragments carefully selected to maximize hit rates. For example:

The company has screened their library against targets such as PTP1B and falcipain-1 and obtained remarkably high hit rates in functional assays. In fact, SerpentesOleum is so confident that they’re offering a money-back guarantee if you don’t obtain at least one active against your target, no matter what it is. Looking at the structures of their compounds, I have no reason to doubt their claim.


MAW said...

The "Universal Reporter" Library! Where is this available? How much does it cost? Sounds like a great way to get preliminary results.

Jonathan said...

Nice one Dan! Almost had me going there....."SerpentesOleum"....very good. They should make sure they include cynaropicrin. The biological activity of this seems to be causing a lot of excitement so this is sure to sell well. Useful as a positive control in everything. Looking at its structure........

Pete said...

This has been an institution for a number of years and just keeps getting better. This is the second year running that I've checked specially. My own contribution this year was to tweet (@pwk2013) the following:

#LigandEfficiency metrics (esp LELP) have secure thermodynamic basis & pharmacological promiscuity is strongly correlated with lipophilicity

Dan Erlanson said...

Thanks for the comments!

This is the second April Fool’s post we’ve devoted to PAINS, but given the number that still (unintentionally) appear in the literature, I think this remains an important topic.

Yes, natural products can be good starting points, but it is important not to be fetishistic about nature: arsenic, strychnine, and lead are all natural – and nasty. Similarly, plenty of organic molecules will inhibit a wide variety of targets, but that doesn’t mean they are good starting points for probes or drugs.

Thymoquinone is a plant-derived compound that can react nonspecifically with proteins, while sulforaphane is an isothiocyanate, which,despite its presence in broccoli, most chemists will think of as a reagent rather than a screening compound. Moving to animals, 4-hydroxynonenal is a product of lipid peroxidation that non-selectively modifies proteins. Finally, toxoflavin and pyocyanine are both bacterial toxins that generate hydrogen peroxide under common assay conditions, and it is this H2O2 that inhibits your favorite protein, not specific binding activity.

The enzymes mentioned (PTP-1B and falcipain-1) are both cysteine hydrolases and thus particularly sensitive to alkylation or oxidation, but I bet these compounds will hit lots of other targets too.

Again, I’m not disputing that these compounds are biologically active. However, as probe molecules (or starting points) they are worse than useless: they are misleading.

jbosch said...

FOL - Fragments of Life by Emerald Bio has been around for some time.