Peptide formation

Dear all

I wonder if someone knows how to code for reacting two amino acids (amide formation) to form a depeptide, specifiying that one amino acid has either a primary amine or secondary amine within a ring (eg. proline)? 

The generic scheme for the reaction below can be:

[NX3;!$(NC~[!#1!#6])]C[C:1]([OH1:2])=O.[H:4][NX3;!$(NC~[!#1!#6]):3]CC(O)=O>>[#7]C[C:1](=O)[N:3]CC(O)=O

If we want to narrow down the acylated nitrogens to primary amines or secondary amines in rings:

[$([NH2X3]),$([NHRX3]);!$(NC~[!#1!#6]):5]C[C:1]([OH1:2])=O.[H:4][$([NH2X3]),$([NHRX3]);!$(NC~[!#1!#6]):3]CC(O)=O>>[N:5]C[C:1](=O)[N:3]CC(O)=O

A little explanation of the first part of above SMARTS (see the attached image as well):

- the nitrogen either has two hydrogens and three connections (primary)

- or the nitrogen has one hydrogen and three connections and in a ring (secondary in a ring)

- but not a nitrogen that is connected to carbon that is connected to a hetero atom (not an amide)

You can run it from the command line in this way, for example displaying the product in MarvinView:

react -r '[$([NH2X3]),$([NHRX3]);!$(NC~[!#1!#6]):5]C[C:1]([OH1:2])=O.[H:4][$([NH2X3]),$([NHRX3]);!$(NC~[!#1!#6]):3]CC
(O)=O>>[N:5]C[C:1](=O)[N:3]CC(O)=O' leucine proline | mview -

Thank you Gyuri

That works perfectly!

Best

Andy

Thank you Gyuri

That works perfectly!

Best

Andy