Wednesday, February 7, 2018

Simple isostere replacement

This post is inspired by a question that came up on the mailing list recently. The poster was looking for help doing bioisotere replacements with the RDKit. The topic is interesting and seems useful enough to merit a short blog post.
In [1]:
# start with the usual imports
from rdkit import Chem
from rdkit.Chem import AllChem, Draw
from rdkit.Chem.Draw import IPythonConsole
import time
from rdkit import rdBase
print(time.asctime())
print(rdBase.rdkitVersion)
Wed Feb  7 15:10:15 2018
2017.09.3
We'll start with some amide (or ester) isosteres taken from here:
In [2]:
isostere_smis = ('[*:1]S(=O)(=O)NC[*:2]',
                '[*:1]C(C(F)(F)(F))NC[*:2]',
                '[*:1]C1CC1NC[*:2]',
                '[*:1]C(F)=CC[*:2]',
                '[*:1]C1COC1NC[*:2]',
                '[*:1]C1COC1OC[*:2]',
                '[*:1]C1=NN=C([*:2])N1',
                '[*:1]C1=NN=C([*:2])O1',
                '[*:1]N1N=NC([*:2])=C1',
                '[*:1]N1N=NC([*:2])=N1',
                '[*:1]C1=NOC([*:2])=N1')
isosteres = [Chem.MolFromSmiles(x) for x in isostere_smis]
Draw.MolsToGridImage(isosteres)
Out[2]:
And now we'll use those to build the reactions that we'll use to apply the bioisosteric transformations.
In [3]:
def buildIsostereReaction(start,replacement):
    qps = Chem.AdjustQueryParameters()
    qps.adjustDegree = False
    qps.adjustHeavyDegree = False
    qps.adjustRingCount = False
    qps.aromatizeIfPossible = False
    qps.makeAtomsGeneric = False
    qps.makeBondsGeneric = False
    qps.makeDummiesQueries = True
    start = Chem.AdjustQueryProperties(start,qps)
    replacement = Chem.AdjustQueryProperties(replacement,qps)
    product = AllChem.ChemicalReaction()
    product.AddReactantTemplate(start)
    product.AddProductTemplate(replacement)
    product.Initialize()
    return product
Create all the reactions and take a look at one of them to get a sense of what we're doing:
In [4]:
amide = Chem.MolFromSmiles('[*:1]C(=O)NC[*:2]')
isostereReactions =[buildIsostereReaction(amide,x) for x in isosteres]
isostereReactions[2]
Out[4]:
Here are the functions for using those reactions:
In [5]:
def doIsostereReplacement(mol,rxn):
    ps = rxn.RunReactants((mol,))
    res = [x[0] for x in ps]
    return res
def doIsostereReplacements(mol,rxns):
    res = []
    for i,rxn in enumerate(rxns):
        seenSoFar=set()
        ims = doIsostereReplacement(mol,rxn)
        p0 = rxn.GetProductTemplate(0)
        # save where the match is
        for im in ims:
            smi = Chem.MolToSmiles(im,True)
            if smi not in seenSoFar:
                im.coreMatches = im.GetSubstructMatch(p0)
                res.append(im)
                seenSoFar.add(smi)
    return res
We'll use capsaicin as our example
In [6]:
mol =Chem.MolFromSmiles('COc1cc(CNC(=O)CCCC/C=C/C(C)C)ccc1O')
mol
Out[6]:
Get all the products of applying our isosteric replacements:
In [7]:
subs = doIsostereReplacements(mol,isostereReactions)
len(subs)
Out[7]:
11
Let's look at what we got back and, though it's mostly obvious, highlight the replacement:
In [8]:
atomsToHighlight = [sub.coreMatches for sub in subs]
Draw.MolsToGridImage(subs,subImgSize=(250,200),highlightAtomLists=atomsToHighlight)
Out[8]:
As I promised above, this is a short one, so that's it for now.
Comments, questions, or pointers to other lists of useful bioisosteres are welcome!

3 comments:

Anonymous said...

Dear Greg,

Thank you for your useful blog post!
I have a question. Bioisosteric replacement is similar to MMP replacement. In rdkit Contrib/mmpa provides mol_tranform.py script. The script can transform query molecules to new molecules with given Matched Pair Rules. In mol_transform.py, AdjustQueryParameters class is not used.
Could you please explain more details about the class if you have time?

Kind regards,
Takayuki

Greg Landrum said...

Hi,

Are you asking for more information about the MMPA code or AdjustQueryParameters()?

-greg

Anonymous said...

Hi Greg,

Thank you for your prompt reply.
That's right. I could understand MMPA code butI would like to know more information about AdjustQueryParameters().

Kind regards,

Takayuki