Disulfide bond patterns in the toxins of spiders of the Ctenidae family. Comparison with Alpha Fold 2.0 predictions

Wandering spiders (family Ctenidae) have multicomponent venoms in which more than 500 different peptides and proteins, called ctenitoxins, have been identified. The main components of the venom are cysteine-rich peptides containing an inhibitory cystine knot (ICK) motif. The pharmacological diversity of ctenitoxins allows us to consider some of them as prototypes for the development of new drugs for the treatment of chronic pain, Huntington’s disease, erectile dysfunction and glaucoma. According to the location of cysteine residues in the amino acid sequence, ctenitoxins are divided into 14 groups containing from 6 to 14 Cys residues. Currently, the spatial structure of only one ctenitoxin, ω-CNTX-Pn4a (Pha1β or Tx3-6) from the Brazilian wandering spider Phoneutria nigriventer, has been determined. Another 10 structural groups of ctenitoxins have homology with the known spatial structures of spider toxins of other families and other proteins, and for three groups the structural homologues are unknown. In this paper, we proposed possible disulfide bonding patterns for all groups of ctenitoxins. A comparison of the obtained schemes with the predictions of the AlphaFold 2.0 program shows that this neural network does not always correctly predict the structures of cysteine-rich peptides, especially if the structures of mature molecules without leader sequences are modeled.