Subject: Re:POSTED RESPONSES: Quantitative assessment of novel ligands

From: Michael Dooley <[email-masked]>
Date: Wed, 28 Jun 1995 16:18:37 +1000 (GMT+1000)

Dear Netters,
	Thanks to everyone who responded to my query
>I'm searching for a protocol or recipe of 'vital statistics' to assess 
>novel ligands that i've designed, so that i'll have firm arguments to 
>convince organic chemists to synthesise a molecule.  I'm using biosym 
>software + intuition to de novo design ligands for a target with good 
>x-ray data and also have access to Oxford Molecular software.  If it 
>might not be possible to roughly predict binding constants for novel 
>compounds that differ greatly from known ligands, are there methods to 
>predict the effects of modifications to known ligands.  I'm aware of 
>scoring functions such as Bohm Comput-aided mol des (1994) 243, but I'm 
>not sure if this would be appropriate. Eagerly awaiting any suggestions. 
*************************************************************************
Michael,
	We have done some preliminary work on assessing binding energies as
calculated from a series of molecular dynamics runs of an inhibitor bound to
the active site of Influenza sialidase. This can be found in J Med Chem 37, 616
(1994) and the work was done by a colleague Neil Taylor. A more comprehensive
paper is at the moment being reviewed for publication in J Comp Chem, but I'm
not sure when that will published.
	I have adapted the protocol Neil developed to several other Sialidase's
and have obtained reasonable results that enable me to at least say whether a
compound is worth proceeding with. The protocol involves a series of molecular
dynamics runs on the inhibitor docked into the active site of the
protein/enzyme of interest and then determining the pairwise non-bonded
interaction energy between the inhibitor and the protein. This enables me to
determine a set relative binding energies. i.e. compound A > compound B >>
compound c = compound d.
	Both Neil and I will hopefully be presenting results at the drug-design
conference later in the year in Cairns. I forgot to mention we used Biosym's
InsightII and Discover for the calculations and viewing of the results.

Bye Jeff.

-- 
Jeff Dyason                                Department of Medicinal Chemistry,
Victorian College of Pharmacy,             Ph:     61 3 9903-9110
Monash University, Parkville,              Fax:    61 3 9903-9582
Melbourne Victoria Australia               e-mail: [email-masked]

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Dear Michael Dooley.

As you are undoubtedly aware there are no simple solutions to your problem.
And the problem is not unique to you, everyone in drug design faces it.
I have just a few comments to make:

We have implemented Boehm's LUDI scoring algorithm (in Sybyl),
and find it somewhat unsatisfactory because it is overly sensitive
to the positions of the atoms, and the hydrogens in particular.
Also, one could wish to make a more sophisticated distinction between
various types of hydrogen bonds.

An inherent deficiency in considering the ligand/protein complex
is that the ligand/water (and protein/water) complexes are
equally important.  To my knowledge the only proper way to treat this
is by means of free energy perturbation calculations (simulations).
Which means hard work or (and ?) good luck to get decent results.

Chemical intuition is likely to be your best tool.
(although an analysis tool like Goodford's GRID is helpful)
But you and your synthetic chemists have to accept that our
ability to predict is not perfect, - it is probably more like
that of the meteorologist making his weather forecast:
better than random.

Sorry, if this sounds awfully pessimistic.

Cheers,

Leif Norskov
Novo Nordisk A/S
Copenhagen
Denmark
[email-masked]

********************************************************************************
     In response to your question - 'what molecular parameters can be 
     generated to convince an organic chemist to synthesise a molecule you 
     have designed?'  
     
     Before embarking on this process you should also view the question 
     from the organic chemists point of view.  He will be considering your 
     compound and prioritising it with other compounds he is already 
     synthesising and will probably make this assessment based on
     
     i)  synthesisability (a major problem with de novo designed ligands)
     
     ii) the state of the project (is it early days and leads are scarce, 
     or is it towards the end of the project when fine tuning is the 
     focus?)
     
     iii) how far is the structure away from the known SAR
     
     iv) in the light of ii and iii what are the chances of success and are 
     the risks worth taking.
     
     There are probably other questions, but I doubt whether any other 
     parameters will make a great difference to your ability to persuade a 
     busy organic chemist to synthesise your compounds.  Presumably you are 
     convinced that the molecules you have designed are worth making, 
     therefore your best approach is to present your argument based on how 
     you have designed the molecules, but most important of all, you should 
     have your chemist collaborators on board at an early stage in the 
     modelling and involve them as much as possible in the process.  
     
     Along with the basic tenet of modelling:
     
     'No modelling without experimentation' (A. Vintner)
     
     we should possibly add:
     
     'No synthesis without dialog' ?!
     
     If you are not convinced yourself that these molecules are worth 
     making and that their synthesis will answer this question, then you 
     need  to get into activity prediction, i.e. QSAR using MOPAC generated 
     parameters, principal component analysis etc, or using Comfa (Tripos). 
     These are not trivial exercises but do give a prediction that may help 
     to decide whether the molecules are worth synthesising.
     
     Good luck anyway!
     
     Chris Snell
     Molecular Modelling and Computational Chemistry
     Sandoz Institute for Medical Research
     5 Gower Place London WC1E 6BN
     
     E-Mail  [email-masked]
     Tel     0171-333-2165
     Fax     0171-387-4116
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Michael,

A program from edusoft called HINT (Hydrophobic Interactions) will give a
rough estimate for the binding constant of a ligand/protein complex.  The
www address is a follows:
	
	http://www.i2020.net/edusoft/hint.html

The nice thing about this program is the "pretty" pictures that can be
generated in order to "validate" your claim for ligand synthesis. In my
experience most synthetic organic chemists seem to love color graphics and
are usually willing to bend over backwards to assist you with your problem
once you provide them with some justification.  The software currently
interfaces with InsightII, Sybyl, and Chem-X.  Also, QSAR analysis can
carry alot of weight with synthetic organic chemists (a standard module in
most software packages).  I would suggest that COMFA QSAR would carry more
weight than standard QSAR. Furthermore, HINT can be used as an additional
COMFA field with QSAR within Sybyl. 

If I can provide further assistance, please drop me a line.  As a side
note, do you know how difficult it is to obtain a post-doctoral position
in your neck of the woods?

I hope that I have been of some help,

Shawn Feaster
University of Iowa
Dept. of Chemistry
[email-masked]
******************************************************************************

There are probably over a hundred citations for the use of CoMFA
as a tool for predicting biological activities (conversely I know
of none for BioSym or Oxford Molecular save that of Boehm and
Richards, the developers). If you are involved with known receptor
structures, some of the work by Garland Marshall and his collaborators,
for example in JACS, might be relevant. Sorry I don't have specific
referebnces handy --
   yet another biased developer, Dick Cramer

[email-masked]
******************************************************************************

A variety of QSAR techniques have been developed for the purpose of predicting
the activity of ligands.  CoMFA, comparative molecular field analysis, is a
relatively new technique which was developed by Dick Cramer of Tripos.  There
is a catch.  Tripos holds a patent on the method and you need a license for
Sybyl for the job.  CoMFA involves the following steps:
1) Generate a set of molecules (learning set + set of new molecules) and
superimpose them.  The hard step is deciding on a reasonable conformation and
determining which atoms to use in the superposition.  You also need to
calculate the charges on the molecule.  MOPAC with the AM1 Hamiltonian works
well.
2) You save the set of molecules with charges in a molecular database.
3) Each molecule in the database is imbedded in a three-dimensional grid.  A
charged probe molecule is placed at each point in the grid and the interaction
energy between the probe and the ligand is calculated at each grid point.  The
three-dimensional matrix of energy values, one per grid point, is called a
field.  Tripos' software divides the energy calculation into two parts: a
steric portion based on van der Waals interactions and an electrostatic part.
4) In the last step, you correlate the biological or chemical activity of the
ligands with the field values.  In effect, each energy at each grid point
corresponds to an "independent variable" so the number of independent variables
far exceeds the number of molecules in the database.  Hence the method of
partial least squares (PLS) is required to construct the model.  In the PLS
algorithm, linear combination(s) of the field values is(are) calculated which
best explain the data.  These linear combinations are the new independent
variables and are called components.  
5) With these components in hand, you can predict the activity of the new
ligands.

I don't guarantee success.  The Martin group at Abbott and the Kubinyi group at
BASF have had extensive experience with the method.  CoMFA did quite well in
modelling logP of amino acids.  I am finishing up a CoMFA analysis of
inhibitors of a serine protease for the Hansch group at Pomona.

Wayne Steinmetz <[email-masked]>
********************************************************************************

I would be very interested to receive a summary of replies. We face similar
problems for the assessment of novel ligands. We have found variants of Bohm's
scoring function useful in conjunction with simple simulation protocols to
check the ligand binds as expected. The problem is that if your set of designs
bind differently and/or have very different chemistry, one needs to have alot
of faith in the ability of current methods to differentiate between them.
However reparametrising Bohm-like scoring functions to agree with experimental
data for the receptor you're interested in should be effective. Of course this
isn't always possible. There's a recent paper by people at Merck who correlated
interaction energies with binding affinities when designing HIV protease
inhibitors and they got nice results.

with thanks
chris
Chris Murray                     | 
Proteus Molecular Design Ltd.,   |  Tel: 01625-500555
Lyme Green Business Park,        |  Fax: 01625-500666
Macclesfield, Cheshire,          |  Email: [email-masked]
SK11 0JL, UK                     |
*********************************************************************************

Dear Michael,

According to your question in CCL about tools for the ligands design,
I want to turn your attention to the program Apex-3D integrated with
insightII (BIOSYM).
It allows among other things to build 3D QSAR models and predict binding
constants for novel compounds.

A short description of the methods incorporated into Apex-3D can be found
in the http://www.dcl.co.il/apex3d.html. More detailed description is
in the Apex-3D Manual available from BIOSYM.
Please feel free to contact me for additional information.

Sincerely yours
	Boris Vesterman

*---------------------------------------------------*
|  Boris Vesterman, Ph.D.                           |
|                                                   |           
|  DCL Systems International Ltd.                   |
|  20 Galgalei Haplada St. Herzlia Industrial Area  |
|  P.O.B. 544 Herzlia 46105 Israel                  |
|  Phone:   972-9-584684                            |
|  Fax:     972-9-543917                            |
|  E-mail:  [email-masked]                         |
*---------------------------------------------------*
*********************************************************************************

If you have a set of related molecules you might be successful with CoMFA.
The best references are to Garland Marshall in J. Med. Chem. His group did
several different test cases.
You could do the calculations with Oxford Molecular ASP/TSAR.
Let me know what other answers you get.

  @@@@@@@@@@@      Yvonne Martin, Senior Project Leader
             @     Computer Assisted Molecular Design Project
   @@@@@@@@  @     D-47E, AP10 2fl
  @          @     Abbott Laboratories
  @          @     100 Abbott Park Road
   @@@@@@@@@@      Abbott Park, IL 60064-3500
                   Phone: 708 937-5362 FAX: 708 937-2625
                   [email-masked]

Andy McCammon wrote a nice review article:

(1)     Straatsma, T. P.; McCammon, J. A., "Theroetical Calculations of Relative
 Affinities of Binding," Methods in Enzymology 1991, 202, 497-511.

[email-masked]
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I further e-mailed Boris (below) and his speedy reply is printed
at bottom.  Thanks Boris!

>Dear Boris,
>        Thankyou for your fast reply to my query on quantit. asess.
>novel ligands.  On the subject of Apex-3D, a member of our group 
>has investigated the application of this software to our problem.
>This avenue is still under investig. but this is our No 1 problem:
> we have many crystal structures of target and ligand and so have very 
>good information on overlays of different ligands.  Apex-3D wants to 
>manipulate our data set away from reality to suit its own ideas on how
>the ligands should align, which seems like a backwards step!  Any ideas?
>Cheers 
>Michael Dooley

 Michael,

I am familiar with this problem. When Apex-3D was created
most of the attention was paid to the "black box" approach,
when no X-ray data are available for enzyme-ligand complex.
Unfortunately in case when you have additional information 
about crystal structures of target and ligand, Apex-3D
still tries to generate its own superposition hypothesis.
You can reduce this list of different biophores by selection
of most appropriate Task Definition parameters and tolerances.
I mean the following: to describe atom_class's and atom_property's
for the specific ligand groups, reduce tolerance ( as narrow
as possible ) to decrease the number of possible alignments.
May be in some cases it is not so simple, and I'll be happy
to answer any questions you have.
BTW, this autumn Apex-3D new version will be shipped ( integrated
with InsightII v.95.0. There is a set of tools for much flexible
task definition and user control of biophore and model selection.
A special tool that is currently under development can help to
solve your problem. It allows to create a biophore from a user
defined superposition. All your suggestion in this direction are
highly appreciated.

Best Regards
        Boris Vesterman

*---------------------------------------------------*
|  Boris Vesterman, Ph.D.                           |
|                                                   |           
|  DCL Systems International Ltd.                   |
|  20 Galgalei Haplada St. Herzlia Industrial Area  |
|  P.O.B. 544 Herzlia 46105 Israel                  |
|  Phone:   972-9-584684                            |
|  Fax:     972-9-543917                            |
|  E-mail:  [email-masked]                         |
*---------------------------------------------------*
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