Funded by: UP-EMERGING INTERDISCIPLINARY RESEARCH (EIDR) PROGRAM
Project Leader: Arturo O. Lluisma, PHD
Conopeptides are gene-encoded peptides found in the venom of Conus species. These peptides act as specific ligands of a variety of ion channels in neuronal membranes, including those in humans, and their significant biomedical potential is well established. The high diversity of venom peptides in Conus makes the diverse species in this genus an important resource for drug discovery. High-throughput DNA sequencing technologies now make it possible to predict the complement of conopeptides produced by a species based on the putative primary structures (i.e., amino acid sequences) inferred from transcriptome sequences. The challenge that this research program seeks to address is how to exploit this wealth of primary structure data to facilitate the determination of the specific biochemical function of those peptides and the realization of their therapeutic potential.
The 3D structural characteristics of ligands determine their ability to bind to specific sites on specific receptors and hence to elicit specific biochemical and physiological effects. Structural characterization of ligands can thus facilitate discovery of their function (in particular, identification of their likely target receptors). Although experimental approaches based on X-ray crystallography and NMR will continue to be essential in the determination of 3D peptide structures, in-silico approaches will be key to addressing the big-data challenge in an efficient fashion. This research program aims to develop such an approach, integrating empirical techniques for peptide structure determination (NMR spectroscopy and mass spectrometry) into a computational pipeline that is designed to yield high-quality predictions of conopeptide 3D structures, predict post-translational modifications, identify structural motifs in conopeptides that are important to receptor recognition, and ultimately predict the likely receptors of these venom peptides.
Project 1: Structural characterization of selected conopeptides using experimental approaches
Project Leader: Lilibeth Salvador-Reyes
Conopeptides are structurally and pharmacologically diverse molecules from the marine gastropods Conus spp. These compounds are validated to be promising leads as drugs and pharmacological probes. To date, more than 1100 conopeptides have been identified. In striking contrast, approximately 10% of these conopeptides have defined 3D structures despite the importance of this structural feature towards the design of more potent analogues. This project aims to purify conopeptides from selected Conus species using a chemistry- and transcriptome-guided approach. The planar structure of the purified conopeptides will be determined using mass spectrometry and the 3D structure using solution-based nuclear magnetic resonance spectroscopy (NMR). The solved structures will be compared to the in silico structural predictions of Project 2.
Project 2: In-silico structural characterization of selected conopeptides
Project Leader: Arturo O. Lluisma
The aim of this project is to develop a computational pipeline that will enable (i) reliable prediction of the 3D structures of certain classes conopeptides from primary sequence data (bearing post-translational modifications), (ii) discovery of common structural features shared by conopeptides that target the same class of receptors, and (iii) development of statistical models for predicting the most likely target receptors of conopeptides given their 3D structures. Experimentally-determined structures (data from PDB and from Project 1 and Project 3) are used as references to validate the structural predictions. The computational tools thus developed will help researchers in the drug discovery community accelerate the process of discovering potential biomedical applications for a large and fast-increasing number of uncharacterized or novel conopeptides that transcriptome sequencing projects have been generating.
Project 3: Transcriptome-peptidome mapping for identification of conopeptides in the Conus venom and prediction of their post-translational modifications
Project Leader: Eizadora Yu-Roberto
Conopeptides undergo post-translational modifications (PTMs) during their maturation in the venom duct. A variety of PTMs have been reported, such as gamma-carboxylation of Glu residues, hydroxylation of Pro, Valine, or Lysine residues, amidation of the C-terminus, or formation of disulfide bonds, among others. Despite the relative ease in the identification of conopeptides based on the expressed DNA sequences thanks to next-generation DNA sequencing technologies, the different PTMs that may be specific to each class of conopeptides are still not straightforward to predict. The ability to predict PTMs of conopeptides is particularly crucial in structural modelling, as the attached functional groups would likely influence the conformational and electrostatic properties of these peptides, and hence their 3D structures, such as those in actual native structures found in Conus venoms.
The project’s aim is to predict PTMs of individual conopeptides by comparing their predicted masses (from the sequences in the transcriptomes) with their actual masses as revealed by mass spectrometry analysis of the peptidome from the same species. The patterns of PTM across different conopeptides or types of conopeptides will also be correlated with sequence features of the peptide precursors to identify potential sequence motifs that may serve as potential signals recognized by PTM enzymes in the venom duct.