tag:blogger.com,1999:blog-1136153439451224584.post5937455842604951527..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: Fragment selectivityDr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-1136153439451224584.post-62784866616957781242011-08-17T12:20:33.690-07:002011-08-17T12:20:33.690-07:00I tend to be wary of selectivity studies. It'...I tend to be wary of selectivity studies. It's not always clear how carefully Km values have been determined and ratios of IC50 values are subject to greater uncertainties than than individual IC50 values. Replicates run from the same DMSO stock solutions are not truly independent and can give an optimistic picture of assay reliability. Check the ITC LinkedIn group discussion starting, 'For enthalpy driven reactions ITC works fine...' to see this last point discussed in more depth.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-87997950160609988842011-08-17T09:03:05.235-07:002011-08-17T09:03:05.235-07:00Regarding assay conditions, the authors state that...Regarding assay conditions, the authors state that "in all activity-based screens the ATP concentration was at or below the Km for the kinase." I think this is fairly standard and makes sense on a theoretical level, though of course extrapolating to cell activity will be more challenging.Dan Erlansonhttps://www.blogger.com/profile/07927082337051189270noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-86377908093841526112011-08-16T19:17:20.546-07:002011-08-16T19:17:20.546-07:00One question that I asked at the 2009 Alderley Par...One question that I asked at the 2009 Alderley Park FBDD conference was to what extent are the properties of fragments predictive of the properties of elaborated fragments. The response was underwhelming and I think that it is still a valid question.<br /><br />When discussing selectivity it's always useful to know what levels of selectivity your assays will allow you to measure. This is a particular issue for fragments which typically bind weakly to their targets. If using biochemical assays to measure kinase selectivity it's worth remembering that assays for different kinases are frequently run at different ATP concentrations and these may well lie outside the typical intracellular range.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-45698744784628735522011-08-16T09:56:38.966-07:002011-08-16T09:56:38.966-07:00These are the sorts of papers that truly push the ...These are the sorts of papers that truly push the art forward. Everyone has a certain bias when it comes to hit selection, no matter the screening technology. Challenging those biases with hard data is always beneficial. Thanks for the commentary, I hadn't seen this paper yet! (Now I learn of papers on blogs before seeing them in an actual journal . . . )Anonymousnoreply@blogger.com