tag:blogger.com,1999:blog-1136153439451224584.post4795483644748177233..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: Ligand efficiency for antibioticsDr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-1136153439451224584.post-87803782250837342192013-04-02T06:54:19.174-07:002013-04-02T06:54:19.174-07:00see the development of this project
"An Impr...see the development of this project<br /><br />"An Improved Small-Molecule Inhibitor of FtsZ with Superior In Vitro<br />Potency, Drug-Like Properties, and In Vivo Efficacy"<br /><br />Neil R. Stokes et all<br /><br />Antimicrobial Agents and Chemotherapy<br />p. 317–325, Volume 57, Number 1<br /><br />alexhttps://www.blogger.com/profile/02494861102571951899noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-41052262496166214822009-01-15T10:20:00.000-08:002009-01-15T10:20:00.000-08:00Dan,My comments on the units of this metric relate...Dan,<BR/><BR/>My comments on the units of this metric relate to the fact that one only can define a logarithm for a pure (i.e. dimensionless) number and not a quantity like 1 mM that has units. Ligand efficiencies defined in terms of non-hydrogen atoms (NHA) use a logarithm of the ratio of an IC50 to some reference concentration. Any reference concentration can be used to define an efficiency and the numbers you get will be determined by the reference concentration used to define efficiency. <BR/><BR/>Writing: <BR/><BR/>LE = (-log(IC50/ref-conc))/NHA<BR/><BR/>shows that all LE metrics defined in this manner have units of reciprocal NHAPeter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-52793754971085038012009-01-15T09:49:00.000-08:002009-01-15T09:49:00.000-08:00I forgot to wish you and Teddy all the best for th...I forgot to wish you and Teddy all the best for the New Year so have a great one!Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-32759542210111443972009-01-15T09:47:00.000-08:002009-01-15T09:47:00.000-08:00This comment has been removed by the author.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-72969815422672032912009-01-13T06:55:00.000-08:002009-01-13T06:55:00.000-08:00Pete - I agree that “antibacterial efficiency” has...Pete - <BR/><BR/>I agree that “antibacterial efficiency” has less physical meaning than “ligand efficiency”: the latter provides a number with units of binding energy per non-hydrogen atom; the former, as you point out, has units that are rather harder to define. Nonetheless, researchers working on antimicrobial research do seem rather wedded to their non-mole based MIC, so an efficiency metric based on this may be more useful to this audience.<BR/><BR/>And as far as “efficiency metric fatigue” goes, I sympathize, but as you’ll see in the next couple posts there’s still some interesting work being done here.Dan Erlansonhttps://www.blogger.com/profile/07927082337051189270noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-3076897195077953732009-01-12T07:13:00.000-08:002009-01-12T07:13:00.000-08:00Great to see that the anti-bacterial folk are yet ...Great to see that the anti-bacterial folk are yet to discover the mole and therefore can give us yet another efficiency metric! I must confess to suffering from 'efficiency metric fatigue'.<BR/><BR/>I was interested to see that the they used natural logarithms to define antibacterial efficiency. Rather worryingly, they quote units for their antibacterial efficiency of mg/ml per non-hydrogen atom.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.com