PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach

Abstract

Fusarium oxysporum remains one of the leading causes of economic losses and poor crop yields; its detection is strained due to its presentation in various morphological and physiological forms. This research work sought to identify novel biomarkers for the detection of Fusarium oxysporum using in silico approaches. Experimentally validated anti-Fusarium oxysporum antimicrobial peptides (AMPs) were used to construct a profile against Fusarium oxysporum. The performance and physicochemical parameters of these peptides were predicted. The gene for the Fusarium oxysporum receptor protein PR-1-like Protein, Fpr1, was identified and translated. The resulting protein model from the translation was then validated. The anti-Fusarium oxysporum AMPs and Fusarium oxysporum receptor protein 3-D structures were characterized, and their docking interaction analyses were carried out. The HMMER in silico tool identified novel anti-Fusarium oxysporum antimicrobial peptides with good performance in terms of accuracy, sensitivity, and specificity. These AMPs also displayed good physicochemical properties and bound with greater affinity to Fusarium oxysporum protein receptor PR-1-like Protein. The tendency of these AMPs to precisely detect Fusarium oxysporum PR-1-like Protein, Fpr1, would justify their use for the identification of the fungus. This study would enhance and facilitate the identification of Fusarium oxysporum to reduce problems associated with poor crop yield, economic losses, and decreased nutritional values of plants to keep up with the growing population.

Analytical Studies of Antimicrobial Peptides as Diagnostic Biomarkers for the Detection of Bacterial and Viral Pneumonia

“…A negative Boman index directly correlates with hydrophobic peptides with a high protein binding potential. Notwithstanding, the positive Boman index in some peptides has been accounted for with the capacity to distinguish HIV in a lateral flow device [ 30 ]. All the mutated peptides exhibited a short half-life because they are not stable, and half-life values as low as one have been reported for AMP molecules used for HIV diagnosis [ 31 ].…”

“…This outcome relates to the work of [ 15 , 16 ], where binding geometry scoring was utilized as the criteria for determining applicant AMPs for pneumonia diagnostics. These perceptions were additionally affirmed utilizing an in-house lateral flow device in which the putative AMPs were utilized to recognize HIV in patient samples [ 30 ].…”

“…Furthermore, the docking interaction results display only the mutated peptides with increased binding potential and atomic contact energy to the respective receptors. As shown in this analysis, these parameters are significant for the determination of novel peptides for detecting diseases through the development of an LFD device [ 30 ]. This research is in line with Williams et al [ 30 ], where parental anti-HIV antimicrobial peptides were mutated using SDM analysis to increase their binding potential against the HIV nucleoprotein, and subsequent molecular validation was carried out for the construction of an LFD device.…”

“…As shown in this analysis, these parameters are significant for the determination of novel peptides for detecting diseases through the development of an LFD device [ 30 ]. This research is in line with Williams et al [ 30 ], where parental anti-HIV antimicrobial peptides were mutated using SDM analysis to increase their binding potential against the HIV nucleoprotein, and subsequent molecular validation was carried out for the construction of an LFD device. Thus, the putative anti-pneumonia AMPs discovered in this research have better binding energy than the parental AMPs.…”

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

“…It was discovered only recently that the wide-ranging functionality of the AMPs against diseases and infections expands the list of activities beyond antimicrobial effects attributed to them ( Zhang and Gallo, 2016 ). AMPs have found applications in diagnostics where they are said to have a wide range of activities against HIV, bacterial and viral pneumonia, and Fusarium oxysporum ( Tincho et al, 2016 ; Williams and Tincho, 2016 ; Bakare et al, 2020 ; Bakare et al, 2021a ; Bakare et al, 2021b ). Therefore, this work aimed to use in silico algorithms such as HMMER to build antimicrobial peptide models against Fusarium solani cutinase 1 for sensitive identification.…”