LATCA

LATCA is collection of ~3600 biologically active small molecules that the Cutler laboratory originally organized for its own internal screening projects. The library is arrayed in 96 well microtiter plates and has been distributed to several labs. It can be used for both assay validation and the identification of known and novel pertubagens of a process of interest. We welcome its use by other labs, and distribute it under the minimally restrictive condition that users eventually send data back to us regarding new bioactivities ascribed to LATCA compounds.

LATCA Presentation



What does LATCA stand for?
Originally, LATCA was intended as an acronym for "Library of AcTive Compounds on Arabidopsis". It could just as easily represent "Library of Annotated Compounds for Arabidopsis". Yes, Sean does like latkes, quite a bit. If anyone can figure out what collection of molecules the acronym GEFILTE (or a reasonable homonym) would be good for, please let Sean know.

How were the compounds in LATCA assembled?
LATCA was assembled in a number of ways. Whole organism, phenotype-based screens of Arabidopsis seedlings were performed using the LOPAC and Spectrum libraries. These were used to identify pharmacological agents from these libraries with activity in Arabidopsis. A screen of a 10K diverse-structure library purchased from Chembridge was additionally performed. Collectively, the hits from these three library screens amount to about 1000 of the compounds in LATCA. An additional 600 compounds were purchased from Chembridge for other projects in the lab and incorporated into LATCA. About 400 "shelf stocks" consisting of herbicides, common inhibitors, plant hormones, research chemicals and other bioactive compounds were included as well. Lastly, ~1600 compounds were obtained by exchanging our compounds for a portion of a library of yeast actives assembled by the Tyers lab. This set contains ~1600 compounds identified as growth inhibitors of S. cerevisiae in a screen against 50K compounds from Maybridge.

How do you define "bioactivity"?
All of the compounds, once assembled, were tested on Arabidopsis with dose curves to assess their potency. The effects of compounds on etiolated hypocotyl length were measured in a simple, quantitative assay to generate IC50 values for all library members. The Cutler lab defines a compound as "active" in this assay if it shows greater than 20% inhibition of hypocotyl length at 100 uM. In addition to the IC50 data, publication quality images were taken of the phenotypes induced by the 3600 LATCA compounds. This data has been used to classify the compound effects into common phenotypic classes such as isoxaben, auxin, oryzalin-like and other classes.

Why would I want to use LATCA?
As is often the case in experimental science, the most important experiment can be the control. In screening experiments, "control" bioactive libraries play an important role. Screening a small collection of bioactive compounds prior to a large scale screen is critical for assay validation and optimization. Additionally, a library of known bioactive compounds can be used to implicate known pathways or target proteins in the process under study. The lab has seen "awesome hits" from diversity-library screens turn out to perturb well characterized pathways through established targets. Establishing this information in advance of a large screening project gives the screener baseline information about what classes of molecules are likely to yield positives in their screen. It can prevent investment in compounds that are not likely to yield new information or targets.

Do you have any general screening tips you could offer me?
Yes, the first installment of Sean's screening tips is available here, check later for more tips.

So, why not just screen the LOPAC and / or Spectrum libraries?
These libraries are excellent screening tools, and LATCA was modeled after them. There are a few major differences to note, however. LATCA is biased towards molecules that are bioactive in plants. More than 50% of the compounds possess bioactivity in Arabidopsis. The hit rate we observed when we screened LOPAC against Arabidopsis was closer to 10%. Additionally, the pathways modulated by LOPAC compounds are biased to those with relevance in mammalian disease biology. Unlike Spectrum and LOPAC, LATCA contains 1000s of novel-structure compounds that have emerged from screens of commercially available diversity libraries. LATCA can therefore inform users about both new and well characterized molecules that affect the assay under study.

What is your lab using LATCA for?
We have used LATCA in a number of microscopy based screens looking for small molecules that affect organelle structure and function. This work was started by a PhD student Simon Alfred. Most recently, Simon has been characterizing a compound named Eroonazole which causes rapid disintegration of ER-tubule integrity. This activity is quite novel and appears to be distinct from the phenotypes caused by many classic perturbagens of the endomembrane system. In general, when a new screen is started in the lab that we ultimately intend to perform on a larger scale, we first screen LATCA to work out kinks in the methodology etc. and to identify known compounds that are active in the assay ("assay validation"). LATCA compounds were also used extensively for our natural variation in drug sensitivity project. We also have a large genetic target identification project underway where we are isolating resistant mutants for >30 compounds from LATCA. If you would like to know if we have isolated mutants for your compound of interest (highly unlikely!), please contact us. If you would like us to add a particular compound to our screening pipeline, also let us know.

How do I restock hit compounds?
The compounds in LATCA are commercially available. Chembridge compounds can be ordered through Hit2Lead, Maybridge compounds through Ryan Scientific, Microsource compounds can be ordered directly from the company. Many of the compounds are carried by multiple vendors, so if you have trouble with resupply, try looking for other vendors using a search engine such as eMolecules (free) or SciFinder Scholar (subscription, but most universities have a site license).

How do I cite my use of LATCA?
An unfinished manuscript describing the assembly and annotation of LATCA has been on Sean's desk for sometime now and will likely make its way into print sometime just before he goes up for tenure review. The main screens used to assemble LATCA are described in this recent Nature Chemical Biology article. We ask that you cite this paper until a formal LATCA publication comes out. According to anonymous sources, more than a few people find it frustrating that Sean has not published on LATCA yet. Well, the latest new is that Simon Alfred, a Cutler lab Ph. D. student from the University of Toronto, is currently writing his dissertation and one of his chapters will present his work using LATCA in microscopy based screens. Sean's current plan is to include the description of LATCA, its assembly and contents in the publication associated with that chapter from Simon's thesis. So if all goes well, summer 2009 will see a formal LATCA paper in print. Sean sincerely apologizes for any inconvenience, frustration or undue duress the delays in publishing LATCA may have caused you or your research.

What format is LATCA distributed in?
LATCA is distributed to other labs in 96 well polypropylene plates as 100X screening stocks in DMSO. The compounds (with a few minor exceptions) are 2.5 mM stocks in DMSO. Our standard distribution set is 47 plates, with each plate containing 80 compounds (columns 1 and 12 empty). 12 ul is sent per well, which is enough for 12 assays, assuming a 100 uL assay volume.

Could I please obtain a set LATCA plates?
In general, we send LATCA out under collaborative terms (at no cost, except that you cover shipping). Keep in mind that LATCA is not a formally funded project and a tremendous amount of work (and resources!) went into assembling it. There is also a substantial amount of work involved in maintaining and distributing the collection. Sean is currently looking into ways to get grant support for the LATCA project; if successful LATCA will be distributed to academic labs without collaborative strings at a very modest cost that covers materials etc. If you cannot wait until then and are not too keen on collaborating with Sean, you might consider purchasing or screening the LOPAC or Spectrum libraries, which LATCA was, in part, modeled after. These tools are present at many screening centers. Alternatively, if you would like to replicate LATCA for your own screening center without having to deal with Sean (a serious pain) you can either (A) wait for the publication on LATCA to come out or (B) deal with Sean. Scenario (B) would involve Sean sending you the contents of LATCA so that you can replicate it. Contact Sean if you are interested in obtaining LATCA.

Could I please get an SDF, DB or PDF of LATCA's contents?
Please contact Sean for this information.

Who contributed to the development of LATCA?
The LATCA project was started by Tsz-Fung (Freeman) Chow, who Sean lovingly refers to as Freebot, on account of his skill at manually doing tasks that a robot really should have performed (if we had had automation in the lab at the time...). Freeman's MSc thesis describes the assembly and characterization of the original ~2000 LATCA compounds. Since that work, the 1600 Tyers lab yeast active compounds were "assimilated" into LATCA and characterized for bioactivity and whole seedling phenotypes in Arabidopsis by Andrew Defries, at the time a technician in my lab. Andrew chooses to program experiments on the Biomek whenever possible, and consequently does not get a "bot" suffix for his name. Andrew is currently a graduate student in the Cutler lab and one of UCR's IGERT trainees. A full list of acknowledgments can be found in the online LATCA slide show.

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