tag:blogger.com,1999:blog-1136153439451224584.post2205886054820253103..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: There can be too much of a Good ThingDr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-1136153439451224584.post-18367540442713787632014-02-17T08:49:23.500-08:002014-02-17T08:49:23.500-08:00I'm just getting back to this post. I was loo...I'm just getting back to this post. I was looking at the nice work from Vulpetti et al. using the local environment of fluorine fingerprints. Are there any large sets of 19F NMR shifts in the literature that can be used for training QSAR models?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-23151203598069312272014-01-18T09:24:22.208-08:002014-01-18T09:24:22.208-08:00"If two compounds bind with same affinity/kin..."If two compounds bind with same affinity/kinetics the S/N will be reduced by 50%."<br /><br />If the S/N if directly related to the fraction of the ligand in the bound state [PL]/[L_total], then this statement is wrong. If two ligands compete for the same site AND are present at the same concentration AND have the same affinity, then the fraction of the ligand in the bound state can still be e.g. 75% of what is used to be in the absence of competitor. If you calculate this competition experiment: [P]=10uM, Kd(L1) = Kd(L2) = 400 uM, [L1]=[L2]=200 uM, then [PL1]/[L1_total] in presence of L2 is 1,24%, in absence it is 1,65%, resulting in 75% of its original value. In case the Kds drop to 10 uM, you are right and the reduction approaches 50%.<br /><br />Hence I believe increasing the bin size even in STD NMR screening is feasible.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-85701439288438922342014-01-17T21:23:53.894-08:002014-01-17T21:23:53.894-08:00With an 19F library of about 2000 compounds and us...With an 19F library of about 2000 compounds and using about 10 compounds per pool, one can still get hit rates upwards of 8-10% with a "druggable" target. No need to screen any higher than 20 uM either (with 10 uM) protein (assuming you have a 19F cryoprobe).Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-15313304563153963512014-01-14T05:54:26.897-08:002014-01-14T05:54:26.897-08:00Michael Goldflam had some comments that I adding f...Michael Goldflam had some comments that I adding for him:<br />Hit Rates: Well, maths doesn't lie. I would suspect that by using mixtures with non-overlapping NMR signals we favor the design of mixtures with compounds that are more diverse, eg have less chances to compete for the same sub-pocket. I dont see why competition is that a big problem. If two compounds bind with same affinity/kinetics the S/N will be reduced by 50%. Depending on the setup you might still detect this. If one compounds is much stronger than the other you might see only the strong one. Normally that are the compounds we focus on right?<br />Finally, if you move from 5 compounds per mixture to 10 why dont we increase the protein concentration x2 as well? This should enable us to see weaker hits and competing compounds.<br />Future improvement in NMR should also allow screening at lower concentrations.<br />Reactivity: Reactivity is a problem but depends how you store/use your library/ library aliquots and the design that you used. If the raction is not driven by DMSO and a truly bimolecular reaction than it has a strong concentration dependence. I think screening large mixtures is only feasible at lower compound concentrations, that would decrease the risk of bimolecular reactivity somehow. Chris mentioned this in the comments on your blog.<br />For the design of our library we used a filter to remove reactive compounds that comes from Vernalis. Obviously you always miss some reactives.<br />Dr. Teddy Zhttps://www.blogger.com/profile/07288045760981372367noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-80612486726698174172014-01-13T11:55:05.416-08:002014-01-13T11:55:05.416-08:00As a CRO, we have a number of constraints to deal ...As a CRO, we have a number of constraints to deal with when screening, such as capacity, plus additional material limitations when utilizing client-provided libraries. For versatility, capacity and throughput, we max out at 10 per designed mixture. This allows immediate deconvolution by 1D ligand screening, and not too much work for HSQC decon, using SO-FAST HMQC. <br /><br />For random pools, the highest we go up to is 4.Darren B.http://www.embios.comnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-31935579905222193572014-01-13T09:03:45.917-08:002014-01-13T09:03:45.917-08:00I just fixed an error in the equation. I just fixed an error in the equation. Dr. Teddy Zhttps://www.blogger.com/profile/07288045760981372367noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-64990508023203657872014-01-13T08:29:37.975-08:002014-01-13T08:29:37.975-08:00Teddy, I should add that I may try to increase the...Teddy, I should add that I may try to increase the pool size after I've run some screens with the new library. Because the concentrations for F19 screening are much lower, cross-reaction and competition may be less severe than what I'm used to seeing with 1H STD NMR. I'd be interested to know what other people have found.Chris Leprenoreply@blogger.com