Long alkyl chains tend to bad things to hang onto any compound, if it's
to be biologically useful. Go consult your friendly local medicinal
chemist, chances are they'll freak out.
Anyway, long alkyl chains LOVE binding to surfaces, which is of course
exactly the sort of thing that generates the signal in SPR. Go consult
your friendly local SPR ligand-binding expert, chances are they'll point
to a number of red flags in your readout - not least the fact that it's
a massive outlier in the chemical series (if I understood your correctly.)
Frank
On 27/04/2018 10:00, Barone, Matthias wrote:
we also do structure-activity relationship and rational drug design.
And I agree with Christian: never rely on one single method and try to
include a homogenous assay, such as ITC or FT. you mention a tyrosine
involved in the binding pocket. Did you try to track the Tyr in FT?
best, matthias
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Christian Roth <christianroth...@gmail.com>
*Sent:* Friday, April 27, 2018 9:00:03 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Compound with flexible conformation but nM Kd
Anectodal evidence I have heard from colleagues working with things,
which are immobilized is that the measured Kd value on the surface can
be wildly different from what is measured in solution. A superbinder
on a surface might not be as good in solution. There seems still a lot
of debate why that is.
Cheers
Christian
On Fri, Apr 27, 2018 at 5:07 AM, WENHE ZHONG
<wenhezhong.xmu....@gmail.com <mailto:wenhezhong.xmu....@gmail.com>>
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
