Hi Greg, I got it to work with my function “get_amide_biosters(smiles)”
which I am happy to share once I clean it up a bit . Sorry I was not clear.
both get_amide_biosters("CC(NC)=O") and get_amide_biosters("CC(OC)=O")
provide the same recursive smiles:
>>
[$(CNC(C)C(F)(F)F),$(CC1=CN=C(C)C=N1),$(CC1=NN=C(C)N1),$(COC(C)=O),$(CC1=NOC(C)=N1),$(CNS(C)(=O)=O),$(COC1C=C(C)ON=1),$(CNC1(C)COC1),$(COC1(C)COC1),$(CC=C(C)F),$(CNC(C)=N),$(CNC(C)=O),$(CC1N=CC=NC=1C),$(CC1=NN=C(C)O1),$(COC1=CC(C)=NO1),$(CC1=CN=CC(C)=N1),$(CNC1(C)CC1),$(CON=C(C)C#N),$(CC1=CN(C)N=N1),$(CNC1=NC=C(C)O1),$(CC1=NN=NN1C)]
This is what I want in order highlight similarity between compounds that
are structurally different but probably biologically similar if they only
differ by a bioisosteric moiety.
Thanks again,
Alexis
On 6 February 2018 at 17:28, Greg Landrum <greg.land...@gmail.com> wrote:
>
>
> On Tue, Feb 6, 2018 at 10:42 AM, Alexis Parenty <
> alexis.parenty.h...@gmail.com> wrote:
>
>> I will try your approach and will nest all the result smiles into a
>> unique recursive smiles.
>>
> I'm not quite sure what you mean here, but it sounds unlikely to work. I
> think you may need to do a SMILES for each of your isosteres.
> After hitting "reply" on the earlier message I realized that this is a
> nice example for a blog post, so I am going to put together some example
> code that you may find useful.
> I would be happy to do the example with your isosteres, but I need some
> kind of explanation of what the actual substitution patterns are. For
> example, you have these three "duplicates" in your original message;
> 'C1=CN=[CH1][CH1]=N1', 'C1=[CH1]N=C[CH1]=N1', 'C1=[CH1]N=[CH1]C=N1'
> Should I interpret these as:
> *C1=C(*)N=CC=N1
> *C1=CN=C(*)C=N1
> *C1=CN=CC(*) =N1
> ?
>
> If that's right, does direction matter? If I apply the second of those
> possibilities - *C1=CN=C(*)C=N1 - to
> ClC(=O)NBr
> should it yield both:
> ClC1=CN=C (Br)C=N1
> and
> BrC1=CN=C(Cl)C=N1
> or just one of them?
>
>
> Best,
> -greg
>
>
>
>
>
> On 6 February 2018 at 07:54, Greg Landrum <greg.land...@gmail.com> wrote:
>>
>>> Hi Alexis,
>>>
>>> If you have substructures with substitutions at a single atom, it tends
>>> to be simpler to use Chem.ReplaceSubstructs to do this. This is, however,
>>> not the case here (or in general for bioisosteric replacement)
>>>
>>> The most flexible way to do what you're looking for is to use the
>>> RDKit's chemical reaction functionality and create one reaction per
>>> isosteric replacement you want to make. Here's a simple example showing the
>>> "amide -> 1,2,3 triazole" replacement:
>>>
>>> In [11]: triazoleRxn = AllChem.ReactionFromSmarts('[*
>>> :1]C(=O)N[*:2]>>[*:1]c1cn([*:2])nn1')
>>>
>>>
>>> And here's how you'd use that to perform a replacement:
>>>
>>> In [12]: ps = triazoleRxn.RunReactants((Chem
>>> .MolFromSmiles('C1CC1C(=O)Nc1ccccc1'),))
>>>
>>> In [13]: Chem.MolToSmiles(ps[0][0])
>>> Out[13]: 'c1ccc(-n2cc(C3CC3)nn2)cc1'
>>>
>>>
>>> Notice that I added the bioisostere itself to the products of the
>>> reaction as SMILES. You don't want query features there.
>>>
>>> I hope this helps,
>>> -greg
>>>
>>>
>>>
>>>
>>> On Mon, Feb 5, 2018 at 10:07 AM, Alexis Parenty <
>>> alexis.parenty.h...@gmail.com> wrote:
>>>
>>>> Dear RDKiters,
>>>>
>>>> I would like to generate the bioisosters of amides from a large list of
>>>> structures:
>>>>
>>>> The smarts patterns for the bioisosters of amides I am interested in
>>>> is:
>>>>
>>>> smarts_path = ['C1=CN=[CH1][CH1]=N1', 'C1=[CH1]N=C[CH1]=N1',
>>>> 'C1=[CH1]N=[CH1]C=N1', 'OC1=[CH1]C=NO1', 'OC1=NOC=[CH1]1',
>>>> 'C1=CN=C([NX3])O1', '[#6X4]([#6X4](F)(F)(F))[NX3]', 'C(C#N)=NO',
>>>> 'N1N=NN=C1', 'N1N=NC=[N]1', 'N1N=NC=[CH1]1', 'C1=NOC=N1', 'C1=NN=C[OX2]1',
>>>> 'C1=NN=C[NH1]1', '[C]1(COC1)[OX2]', '[C]1(COC1)[NX3]',
>>>> 'C([NX3H1])=N[CX4H3]', '[CX4]1([CX4][CX4]1)[NX3]',
>>>> '[#16X4+2]([NX3])([OX1-])([OX1-])', '[#16X4]([NX3])(=[OX1])(=[OX1])',
>>>> '[CX3](=[CX3])(F)', '[OX2][CX3](=[OX1])', '[NX3][CX3](=[OX1])']
>>>>
>>>> How would you best "disconnect the amide moiety" of a structure and
>>>> "replace" it with the recursive smarts pattern of its bioisosters? The
>>>> bioster matching patern above must be contained within a single smarts, so
>>>> I think I need recursive smarts, right?
>>>>
>>>> Any directions would be very much appreciated.
>>>>
>>>> Best,
>>>>
>>>> Alexis
>>>>
>>>>
>>>>
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>>>>
>>>
>>
>
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