In‐Silico Template Selection of In‐Vitro Evolved Kalata B1 of Oldenlandia Affinis for Scaffolding Peptide‐Based Drug Design

Abstract

Structural stability of Oldenlandia affinis cyclotide, kalata B1 of native (1NB1) and two mutants 2F2I ([P20D, V21K] kB1) and 2F2J ([W19K, P20N, V21K] kB1) was investigated. Single model analysis showed high number of intra-molecular interactions followed by more proportion of beta sheet contents in [P20D, V21K] kB1 as compared to that of native and the other mutant of kalata B1. Further, the modern conformational sampling approach, an alternate to classical molecular dynamics was introduced, which revealed that the [P20D, V21K] kB1 was identified as structurally stable one, substantiated by various structural events viz., root mean square deviation, root mean square fluctuation, and angular deviation by Ramachandran plot. Moreover, the statistically validated contours of polar surface area, hydrogen bond distribution and the distance of disulfide bridges also supported the priority of [P20D, V21K] kB1 with respect to stability. From this work, it is proposed that the [P20D, V21K] kB1 (2F2I) could be the best template for scaffolding peptide based drug design.

Cyclotides as drug design scaffolds

“…Such structural studies of cyclotides have mainly involved NMR methods and there are currently 49 entries for cyclotides or related molecules in the PDB, 42 of which were done with NMR and seven with X-ray crystallography. [72][73][74][75][76][77][78][79][80][81][82] and 16 reviews on drug design applications of cyclotides [25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40]. This information is summarised in Figure 1, which provides a schematic illustration of how inputs from fundamental studies of cyclotide synthesis, structure and cell penetration, combined with inputs from the literature on the sequences of bioactive peptides have underpinned applications used to design grafted cyclotides to hit specific targets.…”

The structural and functional reliability of Circulins of Chassalia parvifolia for peptide therapeutic scaffolding

“…Both the structures of Circulin A and Circulin B were energy minimized using YAMBER force field present in YASARA program . The obtained energy minimized structures were used for static structural analysis and for generating conformational ensembles for dynamic analysis …”

“…Circulin A and Circulin B contain six conserved cysteine residues forming three S–S bonds that enrich its stability . Therefore, analyzing the S–S bond distance computationally and their exhibited variations among different conformers obtained through conformational sampling aids in the determination of Circulin stability . The S–S bond distance of cystine knot I, cystine knot II, and cystine knot III varied between Circulin A and Circulin B, as illustrated in Figure .…”

“…10,11,34 Previous studies analyzed the S─S bond distance of cyclic peptides and defined its structural constraint which, in turn, favored the stability. [36][37][38] It was noted that disulfide bonds inflict the geometrical constraints on protein backbones that plays a major role in the structural stability and functionality of proteins. 9…”

“…10,11,34 Therefore, analyzing the S─S bond distance computationally and their exhibited variations among different conformers obtained through conformational sampling aids in the determination of Circulin stability. 37,48 The S─S bond distance of cystine knot I, cystine knot II, and cystine knot III varied between Circulin A and Circulin B, as illustrated in Figure 4. Besides, the variations seen in the S─S bond distance among the obtained conformers was computed using Vega ZZ program.…”