Thanks for the thoughtful thought. The alkyl chain has 8 carbons. The scaffold that the alkyl chain attached to has 3 hydrogen bonds donors and 3 H-bond acceptors and with one phenyl ring. The overall cLogP is around 4 — slightly higher than the Lipinski's rule of five. Yes, I have planed to run the ITC to see what information I can get.
Wenhe > On 27 Apr 2018, at 8:51 pm, vincent Chaptal <vincent.chap...@ibcp.fr> wrote: > > Dear Wenhe, > > A thought came to mind after having read all the other threads, for which I > generally agree. > An alkyl chain on a molecule (charged? hydrophilic?, you mention a negatively > charged binding site) will most likely not lead to micelle formation as the > cmc of the object will be most likely higher than the amount you use in > solution, especially at uM concentrations. But the alkyl chain nevertheless > creates a lot of entropy, it doesn't like being in the water. How long is the > alky chain? if it is 8-9-10 or even 11 carbons, it is likely to be not > hydrophobic enough to want to burry the side chains into a micelle, and be > very exchangeable in solution, yet not happy to be there. Binding onto a > surface would reduce entropy, resulting in a better kon? > You could try ITC, you will have access to detlaH and deltaG of binding, and > by comparing with your other molecules maybe something would come up? > > please correct me if I'm wrong. > > All the best > Vincent > > On 27/04/2018 05:07, WENHE ZHONG wrote: >> Hi Philippe, >> >> The affinity was measured by SPR where we immobilized the protein on the >> chip. One thing I forgot to mention is that the association rate (kon) shown >> in SPR experiment for this compound is faster (>10-fold faster) compared to >> other analogues with similar koff. There is a pi-pi interaction between the >> scaffold structure and the protein (tyrosine ring). Is it possible that the >> hydrophobic substituent could facilitate the formation of this pi-pi >> interaction but not necessary to involve in the interaction? Thanks. >> >> Kind regards, >> Wenhe >> >>> On Apr 27, 2018, at 1:50 AM, DUMAS Philippe (IGBMC) >>> <p.du...@ibmc-cnrs.unistra.fr <mailto:p.du...@ibmc-cnrs.unistra.fr>> wrote: >>> >>> >>> Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG >>> <wenhezhong.xmu....@gmail.com <mailto:wenhezhong.xmu....@gmail.com>> a >>> écrit: >>> >>> Just to be sure: how was the nM affinity evaluated ? By in vitro >>> measurements, or by obtaining an IC50 by tests on cells ? >>> Of course, if you are mentioning an IC50, you may have a measurement of the >>> efficacy of drug entrance in the cells, not just of specific binding to >>> your protein target. >>> Philippe D. >>> >>>> Dear Community, >>>> >>>> A little bit out of topic here. We are applying the structure-based >>>> approach to design compounds that can bind our protein target. We have >>>> synthesized a series of analogues based on the same scaffold with >>>> different substituents at one particular site. The most potent analogue >>>> (nM Kd) has a long alkyl chain substituent. We thought this hydrophobic >>>> substituent should have strong interactions with the target protein >>>> leading to nM range affinity. However, crystal structures show very weak >>>> densities for this substituent and no obvious interaction between the >>>> substituent and the target protein, suggesting that this long alkyl chain >>>> substituent is flexible without binding to the protein. This binding site >>>> is relatively negative charged according to the electrostatic potential >>>> analysis. >>>> >>>> So it is a puzzle to me that how this dynamic and hydrophobic alkyl chain >>>> substituent can lead the compound to achieve nM affinity (>10-fold better >>>> than any other substituent) — in particular the binding site is not >>>> hydrophobic and no interaction is found between the substituent and the >>>> protein. >>>> >>>> Anything I have miss here that can increase the binding affinity without >>>> interacting with the target? >>>> >>>> Thanks. >>>> >>>> Kind regards, >>>> Wenhe >>>> >>>> >>>> >>> >>> >>> >>> >>> >>> >> > > -- > Vincent Chaptal, PhD > Institut de Biologie et Chimie des Protéines > Drug Resistance and Membrane Proteins Laboratory > 7 passage du Vercors > 69007 LYON > FRANCE > +33 4 37 65 29 01 > http://www.ibcp.fr <http://www.ibcp.fr/> > >
