tag:blogger.com,1999:blog-1136153439451224584.post2399639851623833993..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: Fragment library vendors - 2016 versionDr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-1136153439451224584.post-66203361248434251242017-09-11T13:24:40.184-07:002017-09-11T13:24:40.184-07:00We found another vendor of Ro3 Fragment Library, R...We found another vendor of Ro3 Fragment Library, REAXENSE: <br />http://reaxense.com/products/focused-libraries/ro3-fragment-library<br /><br />They have about 1,000 fragmentsAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-59986503457512619862016-06-11T21:49:56.728-07:002016-06-11T21:49:56.728-07:00Upon request, SynphaTec Japon is also importing an...Upon request, SynphaTec Japon is also importing and distributing all Chem-X-Infinity powerful libraries (including fragments) to the Japanese market. For further information about purchase orders, quick and safe deliveries, Japanese scientists can contact us directly at anytime.SynphaTec Japonhttp://www.synphatec-japon.comnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-66399755274321581182016-06-08T03:46:02.408-07:002016-06-08T03:46:02.408-07:00CHEM-X-INFINITY has got also a fragment library. ...CHEM-X-INFINITY has got also a fragment library. <br />For more informations about it. Send your request directly on the Website. Nabil Ghezalnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-54856943685492232752016-06-06T13:11:14.334-07:002016-06-06T13:11:14.334-07:00Thanks for the info Peter and George. The quality...Thanks for the info Peter and George. The quality of the Life Chem library appears to be everything as advertised we are just learning how to handle it better. As I mentioned, I'm not sure that the precipitation was from molecules that were not soluble but probably from the storage and handling of the library. The paper referenced in the post is quite useful to begin to think about how to handle libraries when you receive them.<br /><br />Unfortunately, I don't think there is a one-size-fits-all solution to this issue.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-20811976987863102612016-06-05T19:05:36.952-07:002016-06-05T19:05:36.952-07:00I'm not sure whether sonication is an option f...I'm not sure whether sonication is an option for plated samples although George's suggestion makes sense. Something that one might want to think about in the context of freeze-thaw cycles is how quickly the DMSO stocks freeze. If the freezing rate is faster than the precipitation rate then solutes will effectively remain in 'solution' albeit a solid one. If, however, the solute has time to precipitate before the DMSO has frozen, you'll need to coax that material back into solution after thawing. I don't know if this is something that has been discussed or studied.<br /><br />George, Did you observe any cases of poor solubility in DMSO for particular structural types (e.g. salts)? Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-20468456144558564142016-06-05T14:03:29.046-07:002016-06-05T14:03:29.046-07:00I am George Bondar at Life Chemicals. We do have a...I am George Bondar at Life Chemicals. We do have a library of almost 10,000 fragments that we guarantee to be soluble at 200 mM in DMSO. About 7,000 fragments out of these 10K are also guaranteed to be soluble at 1 mM in aqueous media (PBS). We do real solubility tests in analytical lab. This is done at RT. It is possible that a few fragments crystallized out of solution at -80C. It is most likely that this can be fixed by gentle sonication of these samples at RT or even slightly higher temperature (30-40C). Another reason could be that DMSO absorbed a fair amount of water during several melt/open/re-freeze cycles plates went through. A few fragments that are not guaranteed for aqueous solubility could have partially precipitated because of this. I think sonication at 30-40C will help to nicely re-dissolve these few compounds. Please let me know if this worked. <br /><br />Thank you.<br /><br />GeorgeGeorge Bondarhttp://www.lifechemicals.comnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-30852198141905379022016-06-05T06:50:17.961-07:002016-06-05T06:50:17.961-07:00Just spotted (after 8 years) an absolute howler in...Just spotted (after 8 years) an absolute howler in the DMSO solubility slide that I pointed you towards (the ‘precipitate observed’ and ‘precipitate not observed’ column headings are transposed). Looks like we mentioned DMSO solubility issue in our 2009 <a href="http://dx.doi.org/10.1007/s10822-009-9264-5" rel="nofollow">article</a> which states:<br /><br />“Solubility in dimethylsulfoxide (DMSO) is also an issue because high concentration stock solutions are used. These were checked routinely for evidence of precipitation after delivery to primary liquid store (PLS) as part of the process of assembling GFS05 in soluble form. Precipitate was observed for 29 out of 525 (5.5%) samples registered as adducts but for only 89 of the 4,440 (2.0%) non-adducts. Most samples registered as adducts are salt forms (e.g., sodium salt; amine hydrochloride) so this observation was interpreted as evidence that salt forms were more likely to lead to precipitation from DMSO.”<br /><br />Apologies for the confusionPeter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-17125716420249476662016-06-05T04:49:56.565-07:002016-06-05T04:49:56.565-07:00Just in case it’s relevant, I’ll mention that we o...Just in case it’s relevant, I’ll mention that we observed precipitate in 100mM DMSO stocks when we assembled a large (20k) fragment library at AstraZeneca about 10 years ago. We checked for precipitation (stocks were also shipped to the other three screening centers) before the full library had been solubilized and we noticed that problems appeared to be more likely for salt forms of compounds. We used this information to favor neutral forms in subsequent selections. Slide #19 in this rather dated <a href="http://www.slideshare.net/pwkenny/pwk-fraglib-iqpcoct2008" rel="nofollow">presentation</a> provides some specific details. Another factor to consider is that DMSO is hygroscopic and it is like to become a less effective solvent for organic compounds as its water content increases.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-17527814683978287492016-06-04T19:09:40.214-07:002016-06-04T19:09:40.214-07:00I am new to academia and starting up a lab that ha...I am new to academia and starting up a lab that has a heavy fragment focus. I purchased a subset of the Life Chem library that was supposed to have guaranteed solubility up to 200 mM in DMSO. I had LC plate the library in DMSO at 100 mM. we have used the library to screen against three targets and I have noticed there are several wells with precipitate on them.<br /><br />The library had 50 uL aliquot placed in daughter plates with remaining fragments in the original mother plate for cherry picking. These were stored at -80C and the daughter plates have undergone about 4 freeze thaw cycles. <br /><br />After reading this paper I don't know if the precipitate is from those fragments not being soluble as advertised or from the freeze thaw cycles. I have now moved the library to a refrigerator and will be taking better care of future libraries based on this paper. This is just my two cents. <br /><br />Thanks for the insight and I look forward to meeting all the other FBDD researchers in the future. Maybe at FBLD in Boston!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-2767843692650956462016-06-03T21:52:09.205-07:002016-06-03T21:52:09.205-07:00This blog is like and oasis to me! I just started ...This blog is like and oasis to me! I just started working with fragments and this paper will sure help me out.Marcos Santananoreply@blogger.com