Fragment Library Products and Add-on Services Frequently Asked Questions:

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Additional questions?  Contact us!

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How does Zenobia measure diversity?

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       Zenobia published a three-part blog-series on the different measures of diversity.  Common measure of diversity are discussed in Part 2 and include chemical property diversity, chemical fingerprint diversity and chemical shape diversity. Interestingly, none of these parameters correlate with biological activity.

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       We view high library diversity as an important parameter in increasing the likelihood of obtaining a hit and that the hits that are identified provide a chemically diverse set of starting points for medicinal chemistry optimization. 

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       Towards this end, we have developed our own diversity coefficient named Zen-DC which is the number of unique Murcko cores divided by the number of compounds in the library.  We have the highest Zen-DC of any library on the market (that is available for our internal analysis). A high Zen-DC gives you the highest probability of finding a hit and that the hits you find will provide different chemical series for lead discovery.

 

If more hits are desirable, Zenobia can design follow-on screening libraries of analogues or related cores to expand your SAR and starting points. (back to top)

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What is the diversity of Zenobia's library?

 

       In selecting compounds for our screening libraries, the first filter is chemical properties.  We select from the purchasable chemical database and are not limited to any one vendor. For selection, we follow Zenobia's Guideline of Two to allow plenty of room for optimization into clinical candidates with drug-like properties:  Molecular weight is kept below 200-250, cLogP ≤ 2 and H-bond donors are ≤ 2. The breakdown of chemical property diversity is summarized in our fliers. 

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       Our second selection step is based upon molecular fingerprint diversity.  We cluster compounds based upon molecular fingerprint similarity and then hand select from clusters to maximize core diversity. Final diversity of the library is defined by the Zen-DC as defined below.  A high Zen-DC increases the likelihood of identifying a diverse collection of hits.

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Our Discovery-Library is divided into four unique collections.

 

       Zen-Library 1™ has the lowest Zen-DC because it is heavily biased to cores commonly found in drugs. 

Zen-Library 2™ has a very high Zen-DC and is composed of a collection of unique cores, many with sp3 

centers giving so-called "3D" character.  Zen-Opti™ is the optimum mix of cores found in drugs and more 

complicated sp3 containing cores with no overlap with Zen-Library 1™ and Zen-Library 2™.  Zen-Flex™ is our most unique library with a focus on flexible molecules that can adapt to more complicated 

binding sites and provide directions in lead optimization.

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       The first library in our Express-Line, Zen Core-288™ equally samples all four of our Discovery libraries and provides an ideal entry-point into fragment screening. (back to top​)

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Are your libraries biased to any disease or target class?

       No, the high core diversity and low molecular weight of the libraries are design to increase hit probability for all target classes and the starting points are appropriate for any disease/tissue target. (back to top​)

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What if I have no experience in fragment screening?

       This is not an issue. We offer introductory kits in our Express-line to facilitate rapid access to screening for a small initial investment if you would like to give it a try.  All of the libraries in our Discovery- and Express-Lines arrive pre-plated and reading for screening with minimal set-up time. We also offer screening services and follow-on library design services to enable progression of your hits. (back to top​)

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Do you have an entry-level product I can try before I purchase the full collection?

       Yes! Our Express-Zen-Core288™ is the perfect introductory product.  We provide enough compound for at least one fragment screen pre-plated and ready to go. It equally samples all four libraries in our Discovery-collection.  If you find hits, you may purchase powder for your follow-on validation studies. (back to top​)

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What is the difference between your Express- and Discovery- product lines?

       Zenobia has been building its full Discovery-line of products over the past 10 years. This includes our full 960 compound fragment library collection that includes enough compound to screen multiple targets.  Specifically, the Discovery-line has enough compound to prepare 50 microliters of a 200mM solution. Compounds are shipped as dry film in 96 or 384 well plates.

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       The new Express-line allows for earlier entry into fragment-based lead discovery and currently has one product: Express-Zen-Core288™ which is a 288 compound sampling of the full Discovery line. One microliter of a 200mM stock of each compound is provided in a 384 well plate which should be enough compound for at least one standard assay. (back to top​)

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Can I obtain a copy of the SD files before I purchase?

       All Zenobia SD files are copyright protected and should not be shared without permission from Zenobia.  However, the full Express-ZenCore288™ file may be downloaded from our site.  Sample SD files for the Discovery-line are also available for download from our website.  Please contact us if you would like access to the full Discovery-line SD file in advance of purchase. (back to top​)

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What is the overlap of your library with other commercial vendors?

       Zenobia specifically minimizes incorporation of compounds from other fragment library providers into their collection to minimize the possibility of overlap.  For SD files that are available, there is no significant overlap. Please contact us to inquire about specific library overlap questions. (back to top​)

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What is the format of the library?

       All libraries arrive pre-plated in 96- or 384-well plates.  The Discovery series is delivered as dry film with guidelines for preparing 200mM stocks in the plate. The Express series arrives pre-dissolved in 384 well plates. (back to top​)

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Can I obtain the library in my format?

       Yes, we routinely reformat libraries and provide them in specific plates. We will also pre-dissolve the Discovery series in deuterated or non-deuterated solvents. Please contact us for details. (back to top​)

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Can my student work with this library?

       Yes, we have been told that an attractive quality is that our products are prepared as ready-to-go kits that can be prepared by a student. All libraries arrive with instructions and technical support is available from Zenobia scientists. (back to top​)

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How long does it take to set-up the library for screening?

       The Express-plate arrives ready for screening.  Simply add your assay reagents and run the experiment. For the Discovery-line, 50 microliters of solvent must be added to prepare the compound for screening. This should take 1-2 days through the use of robotics or multichannel pipets and plate shakers. All instructions for solvating the compounds are included with the kit. (back to top​)

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What is the solubility of the compounds in the library?

       All compounds are soluble to 200mM in DMSO (or water) and to 1mM in aqueous solution. (back to top​)

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How much compound is provided?

       For the Discovery-line, 50 microliters of a 200mM solution are provided for approximately 1.5mgs of compound depending on the molecular weight. For the Express-line, 1 microliter of 200mM solution is provided for about 30ng of compound. (back to top​)

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Can I purchase re-supply for my hits?

       Yes, please contact us for information on re-supply. We typically provide dry powder for your hits to enable follow-on experiments but may also supply in plates. (back to top​)

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I have hits, what do I do now?

 

       Congratulations! Zenobia provides guidance on next steps as a consultant service.  By providing us with your hits, we will prepare a series of follow-on libraries for additional screening to improve your potency and establish early SAR. At this time, Zenobia does not provide chemistry services but does have relationships with several providers.  Please contact us for more details. (back to top​)

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Additional questions?  Contact us!