PubChem as a sequence database: Identity search

The previous post introduced the concept of treating PubChem as a sequence database. In that post, structures with the same sequence were collated to search for alternative disulfide bridging patterns. Here we explore the general concept of using sequence identity to search PubChem with the goal of answering the question, what results would (or should) be found for an exact sequence search of a chemical database?

Let’s take for example, kemptide. When written as a sequence, this is represented exactly by LRRASLG:

There are a number of choices to be made when converting a chemical structure to a sequence. For example:
1. We can write uppercase characters for all of D-/L-/DL-amino acids (1a), or we can use lowercase for D- (1b)
2. We can treat sidechain stereochemistry variants of Thr and Ile all as if they were Thr or Ile (i.e. T/I) (2a), or else handle the allo- and ξ versions with ‘X’ (2b)
3. We can consider all sidechain modifications as the parent aminoacid (3a, e.g. Ser(PO3H2) as Ser (and so ‘S’ instead of ‘X’) , instead of distinguishing between them (3b)

If we generate sequences for PubChem following the least specific rules (i.e. 1a, 2a, 3a), then 16 structures are found that have the same sequence as kemptide. These can then be partitioned by generating sequences with more specific rules, for example, distinguishing based on the presence of D- stereochemistry (i.e. 1b, 2a, 3a). As shown below, this first level of separation splits the sequences into those corresponding to LRRASLG, LRraSLG, LrRASLG, lRRASLG and lrRASLG.

In this particular case, only the first of these contains multiple strutures. These can be further split by applying rules 2b and 3b, which here separate based on the phosphorylation of the serines. After this, the ties can be split by considering the IUPAC condensed representation which shows differences in N- and C-terminal modifications, or the presence of a cosolvate.

LRRASLG
    LRRASLG
        Ac-DL-Leu-DL-Arg-DL-Arg-DL-Ala-DL-Ser-DL-Leu-Gly-OH 78069426 acetyl-kemptide
        Ac-Leu-Arg-Arg-Ala-Ser-Leu-Gly-OH 71429096 acetyl-kemptide
        H-DL-Leu-DL-Arg-DL-Arg-DL-Ala-DL-Ser-DL-Leu-Gly-NH2 85062657 kemptide amide
        H-DL-Leu-DL-Arg-DL-Arg-DL-Ala-DL-Ser-DL-Leu-Gly-OH 100074 kemptide
        H-DL-Leu-DL-Arg-DL-Arg-DL-Ala-DL-Ser-DL-Leu-Gly-OH.TFA 118797564 
        H-Leu-Arg-Arg-Ala-Ser-Leu-Gly-NH2 9897033 kemptide amide
        H-Leu-Arg-Arg-Ala-Ser-Leu-Gly-OH 9962276 kemptide
        Unk-Leu-Arg-Arg-Ala-Ser-Leu-Gly-OH 11650926,101224399,101878757 
    LRRAXLG
        H-Leu-Arg-Arg-Ala-Ser(PO3H2)-Leu-Gly-NH2 102212089 [Ser(PO3H2)-5]kemptide amide
        H-Leu-Arg-Arg-Ala-Ser(PO3H2)-Leu-Gly-OH 13783725 [Ser(PO3H2)-5]kemptide
LRraSLG
    LRraSLG
        H-Leu-Arg-D-Arg-D-Ala-Ser-Leu-Gly-OH 53393688 [D-Arg3,D-Ala4]kemptide
LrRASLG
    LrRASLG
        H-Leu-D-Arg-Arg-Ala-Ser-Leu-Gly-OH 99864041 [D-Arg2]kemptide
lRRASLG
    lRRASLG
        H-D-Leu-Arg-Arg-Ala-Ser-Leu-Gly-OH 99864040 [D-Leu1]kemptide
lrRASLG
    lrRASLG
        H-D-Leu-D-Arg-Arg-Ala-Ser-Leu-Gly-OH 99864042 [D-Leu1,D-Arg2]kemptide

Kemptide was chosen here because it’s fairly obscure and so only 16 hits were found. More popular peptides yield many more exact identity hits. For example, oxytocin has 87 hits, octreotide 207 hits, and substance P 608. In fact, turning this on its head, we can also use these exact identity matches to find ‘popular’ peptides that are missing from our internal peptide database.