In silico discovery of biomarkers for the accurate and sensitive detection of Fusarium solani

Abstract

Fusarium solani is worrisome because it severely threatens the agricultural productivity of certain crops such as tomatoes and peas, causing the general decline, wilting, and root necrosis. It has also been implicated in the infection of the human eye cornea. It is believed that early detection of the fungus could save these crops from the destructive activities of the fungus through early biocontrol measures. Therefore, the present work aimed to build a sensitive model of novel anti-Fusarium solani antimicrobial peptides (AMPs) against the fungal cutinase 1 (CUT1) protein for early, sensitive and accurate detection. Fusarium solani CUT1 receptor protein 2D secondary structure, model validation, and functional motifs were predicted. Subsequently, anti-Fusarium solani AMPs were retrieved, and the HMMER in silico algorithm was used to construct a model of the AMPs. After their structure predictions, the interaction analysis was analyzed for the Fusarium solani CUT1 protein and the generated AMPs. The putative anti-Fusarium solani AMPs bound the CUT1 protein very tightly, with OOB4 having the highest binding energy potential for HDock. The pyDockWeb generated high electrostatic, desolvation, and low van der Waals energies for all the AMPs against CUT1 protein, with OOB1 having the most significant interaction. The results suggested the utilization of AMPs for the timely intervention, control, and management of these crops, as mentioned earlier, to improve their agricultural productivity and reduce their economic loss and the use of HMMER for constructing models for disease detection.

Keywords: Fusarium solani; energies; fungus; in silico; protein.

FIGURE 1

Detailed representative structural representation for Antimicrobial peptides (AMPs) model construction.

FIGURE 2

Promising functional motifs present in CUT1 protein predicted by Motif finder (Number of motifs is 3, and it is virulence protein).

FIGURE 3

Structures of the anti-Fusarium solani AMPs and Fusarium solani cut1 protein all represented in ash colour visualized using PyMol.

FIGURE 4

Docking interaction complexes between cut1 receptor protein (represented in blue) and anti-Fusarium solani AMPs (represented in red) visualized using RasMol.