Unveiling the diversity of cyclotides by combining peptidome and transcriptome analysis

Circular peptides have attracted much interest in recent drug development efforts, particularly due to their increased stability over linear counterparts. The family of plant cyclotides represents one of the largest classes of naturally-occurring backbone-cyclized peptides displaying exceptional sequence variability and plasticity around three knotted disulfide bonds. Accordingly, a multitude of pharmaceutically as well as agrochemically relevant bioactivities has been ascribed to them. Their abundance across various species within flowering plants is highlighted by estimated numbers of up to 150,000 different sequences present in single plant families and over 160 at the species level. However, this vast diversity impedes thorough sequence characterization by standard analytical methods using mass spectrometry and thus limits access to a wealth of potentially bioactive compounds that may represent novel lead molecules. Recently the ribosomal origin of cyclotides has been exploited as an alternative way to discover novel sequences. The analysis at nucleotide level allows not only the identification of peptides but also their parent precursor proteins. This combined approach opens access to the discovery of sequences that can provide novel structural templates for a variety of pharmaceutical as well as agrochemical applications. Here we review recent literature related to the discovery of cyclotides. Challenges and opportunities using classical mass spectrometry workflows and novel approaches such as in silico mining will be discussed. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 774-783, 2016.