tag:blogger.com,1999:blog-1136153439451224584.post3162920087115641866..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: 19F Target-based Screening Reduced to PracticeDr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-1136153439451224584.post-49303415220528926162015-02-27T07:12:20.889-08:002015-02-27T07:12:20.889-08:00The 508 cpds screened appear to be non-fluorinated...The 508 cpds screened appear to be non-fluorinated, as only 1 of the 4 hits contained fluorine atoms.<br /><br />Shouldn't we consider work from Fesik's groups to also be target-based ligand screening? Perhaps what is first about this paper is the screen against a fluorine-labelled protein?Matthew R. Leehttps://www.blogger.com/profile/09787307466209873125noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-52027117470660733672015-02-27T04:53:44.146-08:002015-02-27T04:53:44.146-08:00As usual in NMR, any experiment works well for ubi...As usual in NMR, any experiment works well for ubiquitin, lysozyme, or similarly sized proteins (12 kDa in this case). Good luck getting this running for a 'regular' drug target (usually 35 kDa or bigger). The 19F relaxation will kill the signal and sensitivity will be much lower than proton detect experiments on the protein. So this can be a nice technology addition, for fairly small proteins. Stephan Zechnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-25204803625917835162015-02-20T14:45:43.481-08:002015-02-20T14:45:43.481-08:00thanks for taking the time to answer
much obliged...thanks for taking the time to answer <br />much obliged <br />jJacobhttps://www.blogger.com/profile/01514245140211506410noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-36659867928101621042015-02-20T13:53:02.490-08:002015-02-20T13:53:02.490-08:00We looked at an old sequence alignment of other KI...We looked at an old sequence alignment of other KIX domains from a nice paper by the Naar group. A lot of the aromatics seem to be conserved, so probably worth a try. In general the protein protein interaction <br />field has seen a large enrichment of aromatics (particularly Y and W) at PPI interfaces, which is why we decided to label them.<br /><br />Anonymoushttps://www.blogger.com/profile/05133550270835964706noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-60379154982492362142015-02-20T13:20:21.097-08:002015-02-20T13:20:21.097-08:00Dr. Pomerantz, While your here any thoughts on how...Dr. Pomerantz, While your here any thoughts on how the results might translate to the hit rates of other Kix domains such as MED15 (PBDID:2GUT) or GAL11 (PDBID:2K0N)?Jacobhttps://www.blogger.com/profile/01514245140211506410noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-56830439740767402152015-02-20T13:13:48.080-08:002015-02-20T13:13:48.080-08:00Mostly just being concerned that as with any modif...Mostly just being concerned that as with any modification its not an artifactual consequence.<br />I was hoping for an simple check (ex. you can tell from the shift that is or isn't a contact point)-- While its not a major issue if one wants to check it sounds like there is no easy way out, a second assay is needed (NMR or otherwise)Jacobhttps://www.blogger.com/profile/01514245140211506410noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-3172082847171987292015-02-19T17:53:10.442-08:002015-02-19T17:53:10.442-08:00One trick we have done, is change the fluorinated ...One trick we have done, is change the fluorinated amino acid labeling approach you use to monitor the binding event, such as 3-fluorotyrosine, to either 4-fluorophenylalanine or 5-fluortryptophan (or even a different isomer of fluorotyrosine) in the binding site, and compare the Kd. You can also use a complementary method without fluorine to compare. We haven't seen significant effects yet, but it doesn't mean they can't occur.Anonymoushttps://www.blogger.com/profile/05133550270835964706noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-14187586636334492472015-02-19T14:09:20.107-08:002015-02-19T14:09:20.107-08:00Are you thinking hydrogen bonding through fluorine...Are you thinking hydrogen bonding through fluorine? I would expect this NOT to be the case, but there is no reason why it couldn't be contributing. Dr. Teddy Zhttps://www.blogger.com/profile/07288045760981372367noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-39917113424181346882015-02-19T13:24:48.686-08:002015-02-19T13:24:48.686-08:00With such a technique is the an easy way to check ...With such a technique is the an easy way to check that the Fluorine modification isn't the primary contributor to the interaction?<br />(or is it obvious that there not and I's just missing it?)Jacobhttps://www.blogger.com/profile/01514245140211506410noreply@blogger.com