Cyclotide Structure–Activity Relationships: Qualitative and Quantitative Approaches Linking Cytotoxic and Anthelmintic Activity to the Clustering of Physicochemical Forces
Figure 2
Flow chart depicting the methodology used for QSAR modeling.
Predicted structures for the cyclotides were obtained through homology modeling using the sequences of the 13 cyclotides whose solution-phase structures had previously been determined by NMR. A) To identify appropriate templates, each target sequence was aligned with those of the 13 peptides with known structures. A neighbor joining (NJ) tree was then constructed based on the multiple sequence alignment. The resulting cladogram was used to identify the closest relatives of the target sequence with a known structure, which were then used as templates for modeling the unknown structure of the target peptide. B) For each template sequence, 20 PDB structures were generated based on the pairwise sequence alignment of the target sequence with the selected templates. These 20 conformations were evaluated using the DOPE potential and GA341 score, and the best three conformations were selected. If two templates were chosen for a target sequence, a total of 6 PDB structures were selected. C), D) and E) The structures generated during step B were subjected to conformation searches. If structural refinement of the protein as a whole yielded a result with an unacceptable geometry or one for which the RMSD of the Cα-atoms was greater than 2.0 Å relative to the starting conformation, two loops were selected for loop sampling. Loops were selected based on their sequences, focusing on those containing residues with different physicochemical properties relative to those in the corresponding positions of the template sequence or those that aligned with gaps in the template sequence. After structure refinement, one conformation of each peptide sequence was selected for use in calculating the molecular descriptors. The molecular descriptors of the cyclotides, together with their activity data were used as variables in QSAR modeling.