Title:In Silico Analysis of Natural Plant-Derived Cyclotides with Antifungal
Activity against Pathogenic Fungi
Volume: 31
Issue: 3
Author(s): Akshita Sharma, Bisma Butool, Pallavi Sahu, Reema Mishra and Aparajita Mohanty*
Affiliation:
- Department of Botany, Gargi College, University of Delhi, Delhi, India
Keywords:
Antifungal, cyclotides, cycloviolacin O2, cycloviolacin O13, hydrophobic cluster, membrane-cyclotide interaction, tricyclon A.
Abstract:
Background: Fungal infections in plants, animals, and humans are widespread across
the world. Limited classes of antifungal drugs to treat fungal infections and loss of drug efficacy
due to rapidly evolving fungal strains pose a challenge in the agriculture and health sectors.
Hence, the search for a new class of antifungal agents is imperative. Cyclotides are cyclic plant
peptides with multiple bioactivities, including antifungal activity. They have six conserved cysteine
residues forming three disulfide linkages (CI-CIV, CII-CV, CIII-CVI) that establish a Cyclic Cystine
Knot (CCK) structure, making them extremely resistant to chemical, enzymatic, and thermal
attacks.
Aim: This in silico analysis of natural, plant-derived cyclotides aimed to assess the parameters
that can assist and hasten the process of selecting the cyclotides with potent antifungal activity and
prioritize them for in vivo/ in vitro experiments.
Objective: The objective of this study was to conduct in silico studies to compare the physicochemical
parameters, sequence diversity, surface structures, and membrane-cyclotide interactions
of experimentally screened (from literature survey) potent (MIC ≤ 20 μM) and non-potent (MIC >
20 μM) cyclotides for antifungal activity.
Methodology: Cyclotide sequences assessed for antifungal activity were retrieved from the
database (Cybase). Various online and offline tools were used for sequence-based studies, such as
physicochemical parameters, sequence diversity, and neighbor-joining trees. Structure-based
studies involving surface structure analysis and membrane-cyclotide interaction were also carried
out. All investigations were conducted in silico.
Results: Physicochemical parameter values, viz. isoelectric point, net charge, and the number of
basic amino acids, were significantly higher in potent cyclotides compared to non-potent cyclotides.
The surface structure of potent cyclotides showed a larger hydrophobic patch with a higher
number of hydrophobic amino acids. Furthermore, the membrane-cyclotide interaction studies
of potent cyclotides revealed lower transfer free energy (ΔG transfer) and higher penetration depth
into fungal membranes, indicating higher binding stability and membrane-disruption ability.
Conclusion: These in silico studies can be applied for rapidly identifying putatively potent antifungal
cyclotides for in vivo and in vitro experiments, which will ultimately be relevant in the agriculture
and pharmaceutical sectors.
