Hi Greg,
Thanks a lot for your response, it helps a lot. I indeed notice it was more
difficult with two attachment point (I got it working with acid
bioisosters, one attachment point but could not make my head around with
two). I will try your approach and will nest all the result smiles into a
unique recursive smiles.
Best,
Alexis
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)Nc1c
> cccc1'),))
>
> 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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