Efficacy of sodium silicate on Aspergillus flavus and its action on cell wall degrading enzymes with molecular docking studies

Abstract

The extent of spoilage of fruits and vegetables increases post harvest, and fungi is one of the greatest causes. The effect of sodium silicate on Aspergillus flavus and its cell wall degrading enzymes, namely polygalacturonic acid transeliminase (PGTE), pectin methyltranseliminase (PMTE), and pectin lyase (PL), was investigated via molecular docking. At the 4^th day, 100 mM of sodium silicate completely inhibited A. flavus, while it reflected 79.70, 61.16, 56.82, and 37.23% inhibition at 6, 8,10, and 12 days, respectively. The PGTE (369.33 ± 2.08 U/mL) showed maximum activity at 8^th day in the medium without sodium silicate, also at 20 to 80 mM sodium silicate, their maximum activity was recorded at the 8^th day, while it reached to maximum at 10^th day in the medium with 100 mM sodium silicate. The PMTE recorded highest activity at the 6^th day (414.00 ± 1.73 U/mL) without sodium silicate, at 8^th day when sodium silicate ranged from 20 to 80 mM, and at 10^th day (97.67 ± 1.25 U/mL) with 100 mM sodium silicate. Day 8 was optimum for PL activity. Sodium silicate demonstrates potent interaction with the active sites of the studied proteins, suggesting its potential as a molecular inhibitor of studied enzymes.

Full Article

Efficacy of Sodium Silicate on Aspergillus flavus and its Action on Cell Wall Degrading Enzymes with Molecular Docking Studies

Aisha M. H. Al-Rajhi ,^a,* Abeer S. Albalawi,^b,c Nahlah N. Albakri,^b,c Abeer M. Almutrafy,^b,c Ahmad Alhujaily,^b Soad K. Al Jaouni,^d, and Samy Selim ,^e,*

The extent of spoilage of fruits and vegetables increases post harvest, and fungal attack is one of the greatest causes. The effect of sodium silicate on Aspergillus flavus and its cell wall degrading enzymes, namely polygalacturonic acid transeliminase (PGTE), pectin methyltranseliminase (PMTE), and pectin lyase (PL), was investigated via molecular docking. On the 4^th day, 100 mM of sodium silicate completely inhibited A. flavus, while it reflected 79.70, 61.16, 56.82, and 37.23% inhibition at 6, 8,10, and 12 days, respectively. The PGTE (369.33 ± 2.08 U/mL) showed maximum activity at the 8^th day in the medium without sodium silicate. Also at 20 to 80 mM sodium silicate, their maximum activity was recorded at the 8^th day, while it reached to maximum at the 10^th day in the medium with 100 mM sodium silicate. The PMTE recorded the highest activity at the 6^th day (414.00 ± 1.73 U/mL) without sodium silicate, at the 8^th day when sodium silicate ranged from 20 to 80 mM, and at the 10^th day (97.67 ± 1.25 U/mL) with 100 mM sodium silicate. The maximum PL activity was recorded on day 8. Sodium silicate demonstrates potent interaction with the active sites of the studied proteins, suggesting its potential as a molecular inhibitor of studied enzymes.

DOI: 10.15376/biores.20.2.3996-4008

Keywords: Sodium silicate; Fungi; Docking studies; Polygalacturonic acid transeliminase; Pectin lyase; Spoilage; Fruits

Contact information: a: Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; b: Department of Biology, College of Science, Taibah University, Al Madinah, 42353, Saudi Arabia; c: Health and Life Research Center, Taibah University, Madinah 42353, Saudi Arabia; d: Department of Hematology/Oncology and Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia; e: Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia;

* Corresponding author: amoalrajhi@pnu.edu.sa (A.M.H.A.); sabdulsalam@ju.edu.sa (S.S.)

INTRODUCTION

Fungi are among the most significant factors that contribute to the deterioration of fresh vegetables and fruit. Various products of nutrition, including vegetables, seeds, and dry and fresh fruits are affected by Aspergillus flavus and their toxins, which are known as aflatoxins (Segura-Palacios et al. 2021). Such toxins are potent carcinogens, and they are extensively controlled in numerous countries (Samaila et al. 2018; Zakaria et al. 2024). To create a complex network and colonize the plant tissues, the pathogen typically needs to break through the cell walls of the plant. Certain fungal pathogens release cell wall degrading enzymes (CWDEs) during this process to break down the elements of plant cell walls, facilitating the pathogen’s entry into the cell (Xue et al. 2018; Zhang et al. 2021). Fruit softening is regulated by CWDEs, including endo-1,4-𝛽-D-endoglucanase (EGase), xyloglucan endotransglucosylase (XET), 𝛽-galactosidase (𝛽-gal), cellulase (Cx), polygalacturonase (PG), pectin methylesterase (PME), polygalacturonic acid transeliminase (PGTE), pectin methyltranseliminase (PMTE), and pectate lyase (PL). Both PGTE and PMTE remove the hydrogen at C5 by cleaving the α-1,4-linkage between the methylgalacturonides in the pectin molecule. While PMTE targets methylated polygalacturonic acid or pectin in the cell wall, PGTE specifically cleaves the α-1,4-glycosidic bond within the pectinate molecule. Research has demonstrated that fungi including Colletotrichum gloeosporioides and Botrytis cinerea secrete a variety of CWDEs, such as PG, PME, and PL. The mechanisms used by fungi to regulate the secretion of CWDEs have not been well documented.

Silicon is the second major element on Earth, representing 0.1 to 10% in plant’s dry weight and impacts disease resistance in plants. Applying sodium silicate after harvest inhibits fungal fruit deterioration (Zhou et al. 2018). However, knowledge of its exact mode of action regarding the induction of plants to suppress fungal pathogens is still limited. Si contributes to the host-pathogen interaction metabolically by boosting the activities of plant defense enzymes, which increases the accumulation of defensive compounds such as phytoalexins and phenolics, thus strengthening the plants’ resistance to biotic and abiotic stressors (Reynolds et al. 2016). The composition of soil fungal and bacterial communities was also altered by sodium silicate (Na₂SiO₃); in particular, it reduced the relative abundances of microbial taxa that contained plant pathogens while increasing those that had potential benefits for plants (Zhou et al. 2018; Rayón-Díaz et al. 2021). Zhang et al. (2021) recorded the inhibitory action of both sodium silicate and chitosan individually against Alternaria alternata, but their combination proved more effective than chitosan alone. Moreover, the natural rate of rotting of winter jujube by A. alternata was decreased as a result of sodium silicate and chitosan. Currently, an important and accessible form of computational chemistry is molecular docking. It is beneficial to look at a specific drug candidate’s potential action mechanism and target interactions (Al-Rajhi et al. 2022a, 2022b; Qanash et al. 2022; Yahya et al. 2022; Alghonaim et al. 2023; Qanash et al. 2023; Al-Rajhi et al. 2024). The purpose of this study was to evaluate the influence of sodium silicate on decaying fungus of apple fruits, as well as their effect on CWDEs activity via molecular docking studies.

EXPERIMENTAL

Fungus Isolation and Identification

Apple fruits exhibiting spoilage were collected from fruit markets of Riyadh region, Saudi Arabia. Small segments of spoiled fruit were sterilized employing hypochlorite (1%) for 2 min (for killing the spores on the fruit surface from air but not killing the invaded fungal mycelia within the tissues). Then, the segments were placed on the surface of potato dextrose agar (PDA) medium, followed by incubation at 30 °C. The fungus was recultivated for purification process at the same conditions of the isolation process. The purified fungus was identified according to Raper and Fennell (1973) and Samson et al. (1995), depending on the morphological and microscopical features including shape, color, texture of colonies, diameter, and form of conidiospores, hyphae, and phialide.

Growth of A. flavus at Different Doses of Sodium Silicate

Supplemented PDA (SPDA) medium with different doses 20, 40, 60, and 100 mM of sodium silicate was prepared. Active discs (6 mm radius) from cultivated PDA with A. flavus for 5 days were transferred to the center of plate containing SPDA, followed by incubation up to 12 days. The diameter of the developed colony was detected at each period of incubation.

Preparation of Crude Enzyme Extracts of A. flavus

Czapek’s-Dox broth medium containing sodium silicate (80 mM) was inoculated with A. flavus. The culture was incubated at 30 °C under shaking condition (120 rpm) for a period between 4 to 12 days. The control was applied using medium lacking sodium silicate. At the end of the incubation period, the broth medium was centrifuged for 25 min, at 4 °C and at 10,000 g. The supernatant functioned as the crude enzymes.

Assay CWDE Activities of A. flavus

With minor changes, according to Yang et al. (2012), the activities of polygalacturonic acid transeliminase (PGTE) and pectin methyltranseliminase (PMTE) were recorded. The required substrates for PGTE and PMTE were polygalacturonic acid and pectin, respectively. The following contents 0.3 mL of 1 mg/mL polygalacturonic acid or pectin, 1 mL of 3 mM CaCl₂, 4 mL of Gly–NaOH (50 mM, pH 9) buffer, and crude enzyme (100 μL) were mixed to start the enzymes reaction. At 30 °C, the mixture was incubated for 5 min. The activities of enzymes were expressed as U/mL. With minor changes, according to Jia et al. (2009), the activities of pectin lyase (PL) were recorded. The contents of the reaction mixture were 0.5 mL of crude enzyme and 2.0 mL of 0.5 mg/mL pre-incubated pectin at 40 °C for 5 min. Then, the reaction mixture was kept for 10 min at 40 °C. For ending the reaction, 7.5 mL of HCl (10 mM) was added.

Molecular Docking

Molecular docking was performed to investigate the affinity of sodium silicate against pectin lyase, pectin methyltranseliminase, and polygalactronase. The chemical structure of sodium silicate was drawn using ChemDraw Ultra 15.0. The 3D structures of the target proteins pectin lyase (PDB ID: 1IDJ), pectin methyltranseliminase (PDB ID: 3OQB), and polygalacturonase (PDB ID: 1K5C) were obtained from the Protein Data Bank (PDB). The following steps were carried out to prepare the protein structures:

1. All non-protein components, such as water molecules and bound ligands, were removed.
2. Hydrogen atoms were added, and protonation states were adjusted according to physiological pH.
3. The structures were energy-minimized to relieve any steric clashes.
4. The site finder created the active binding sites, which served as the binding pocket’s dummy sites.

Preparation of ligand (sodium silicate)

1. The ligand structure was created and optimized to achieve a low-energy conformation.
2. Partial charges were assigned, and the geometry was optimized using a molecular mechanics force field.

Docking Procedure

Sodium silicate was placed at the site using the triangle matcher method, and the stiff receptor atoms were docked for 100 ns. The GBVI/WSA dG procedures were employed for rescoring, and the London dG served as a scoring function. Multiple poses were generated for each ligand-protein pair, and the top five ranked poses were selected for detailed analysis.

The 2D and 3D interaction diagrams were generated to visualize the binding modes of sodium silicate within the active sites of each protein. These visualizations highlighted specific interactions, such as hydrogen bonds and metal-ligand interactions.

The docked complexes were analyzed to determine the interactions between sodium silicate and the active site residues of the proteins. Hydrogen bonds, hydrophobic interactions, and metal coordination were identified. Key interaction parameters, such as bond distances and interaction energies, were recorded.

Statistical Analysis

The findings were offered as mean ± standard deviation (SD) by Microsoft Excel 365 and SPSS v.25.

RESULTS and DISCUSSION

The isolated fungus from decayed fruits of apple was identified as A. flavus. This fungus has been isolated previously from various fruits, vegetables, grains, and seeds (Mailafia et al. 2017; Samaila et al. 2018; Abdelghany et al. 2020; Al-Rajhi et al. 2023; Zakaria et al. 2024). The application of different doses of sodium silicate evidently inhibited A. flavus growth with larger inhibitory action at high doses. The colony development of A. flavus treated by 100 mM of sodium silicate was completely inhibited up to the 4^th day, and showed 12.25, 25.50, 30.60, and 45.26 mm at 6, 8,10, and 12 days with inhibition levels 79.70, 61.16, 56.82, and 37.23% (Table 1). Moreover, from Table 1, as the incubation period increased, the resistance of A. flavus to sodium silicate increased. At 60 and 80 mM of sodium silicate, there was no growth on the 2^nd day, but it appeared afterwards. Sodium silicate was applied previously to control the fungal growth such as Fusarium sulphureum (Li et al. 2009), Trametes versicolor (George 2009), and Harpophora maydis Farahat (2019). Remarkable changes appeared in the structures of A. flavus exposed to sodium silicate, where the diameter of conidial head, vesicle, and hypha, besides the length of phialides, were decreased with increasing dose of sodium silicate (Table 2). This outcome was consistent with the examination of Li et al. (2009) and Ge et al. (2017). They observed that sodium silicate at 100 mM completely prevented the Fusarium semitectum and Trichothecium roseum growth, respectively. Additionally, sodium silicate showed a suppressed effect on Geotrichum citri-aurantii growth (causing sour rot of citrus fruit) (Li et al. 2019).

Table 1. Growth of A. flavus under Different Concentrations of Sodium Silicate and Incubation Periods

Table 2. Morphological Characterization of A. flavus at Different Doses of Sodium Silicate

From Table 3, the maximum activity of PGTE was recorded at the 8^th day in the medium without sodium silicate (369.33 ± 2.08 U/mL) and the medium with sodium silicate ranged from 20 to 80 mM, while it reached maximum at day 10 in the medium with 100 mM sodium silicate and then decreased with increasing period of incubation. Their activity level at the 8^th day under 100 mM of sodium silicate regarding the control (100%) was 33.1%. Additionally, the activity of PMTE increased with an increase in the period of incubation up to 6 days for the control (414.00 ± 1.73 U/mL), 8 days for the specimen supplemented with sodium silicate from 20 to 80 mM (363.00 ± 3.00 to 136.33 ± 0.58 U/mL), and 10 days for medium supplemented with 100 mM sodium silicate (97.67 ± 1.25 U/mL) (Table 4). Their activity level at the 8^th day under 100 mM of sodium silicate regarding the control (100%) was 14.0%. At the 8^th day, the maximum activity of PL was detected in the medium without (787.67 ± 2.31 U/mL) or with different concentrations of sodium silicate (Table 5).

Table 3. Activity of PGTE (U/mL) at Different Doses of Sodium Silicate and Different Incubation Periods

Table 4. Activity of PMTE (U/mL) at Different Doses of Sodium Silicate and Different Incubation Periods

Table 5. Activity of PL (U/mL) at Different Concentrations of Sodium Silicate and Different Incubation Periods

Their activity level on the 8^th day under 100 mM of sodium silicate regarding the control (100%) was 48.9%. Generally, the activity of CWDEs, namely PGTE, PMTE, and PL, was affected by sodium silicate at all incubation periods. Such enzymes (CWDEs) are regarded as pathogenicity agents that participate in fruit and vegetable decay caused by several fungi. According to Ge et al. (2017), sodium silicate possesses inhibitory action on the activity of CWDEs. González-Jiménez et al. (2023) mentioned that sodium silicate controlled the citrus fruit decaying via their effects on CWDEs.

The docking study focused on the interaction of sodium silicate with three specific proteins: Pectin Lyase (PDB ID: 1IDJ), Pectin Methyl transeliminase (PDB ID: 3OQB), and Polygalacturonase (PDB ID: 1K5C), as illustrated in Fig. 1. The key docking parameters, including docking scores, interaction types, binding energies, and distances, were analyzed to evaluate binding affinities and interaction mechanisms, as presented in Tables 6 and 7.

Docking Scores and Binding Energies

1IDJ (Pectin Lyase) showed docking scores ranging from -3.69269 to -4.34457, with energy contributions highlighting a mix of hydrophobic and electrostatic interactions.

3OQB (Pectin Methyltranseliminase) exhibited scores from -3.80886 to -4.04268, suggesting strong stability in binding.

1K5C (Polygalacturonase) had scores from -3.81369 to -4.46592, indicating slightly stronger binding compared to 3OQB.

All proteins demonstrated favorable energy contributions, especially from E_conf and E_place, emphasizing stable conformations upon docking.

Interaction Analysis

1IDJ: Sodium silicate formed hydrogen bonds and metal interactions with Aspartate (ASP 154) and Valine (VAL 101), showing short interaction distances (2.78 to 3.07 Å) with low binding energies (-0.7 to -1.5 kcal/mol).

3OQB: Strong hydrogen bonding and metal coordination were observed with residues, such as Arginine (ARG 185) and Glutamate (GLU 113), with distances ranging from 2.77 to 2.95 Å and energies as low as -4.9 kcal/mol.

1K5C: Interactions were observed with Lysine (LYS 228) and Aspartate (ASP 153, ASP 173), having distances of 2.65 to 2.92 Å and binding energies ranging from -1.0 to -3.1 kcal/mol.

The docking results highlight that sodium silicate exhibits significant binding affinity and stability across all three enzymes. The strong binding of sodium silicate can be attributed to the following:

1.  Energy Contributions:

The favorable E_place and E_conf values underscore the ability of sodium silicate to fit well into the active sites of these proteins.

The binding energies, particularly those involving hydrogen bonding and metal coordination, are indicative of specific and strong interactions with catalytic residues.

2. Specific Interactions:

Residues such as ASP and GLU are crucial in stabilizing sodium silicate because of their ability to coordinate metal ions effectively.

The low RMSD_refine values (< 4 Å for most configurations) suggest minimal structural deviations post-docking, confirming stable complexes.

3. Comparative Binding Strength:

Polygalacturonase (1K5C) exhibited the highest binding score (-4.46592), which may be due to more favorable metal interactions compared to other proteins.

The interaction energy for Pectin Methyltranseliminase (3OQB) was notable, especially for ARG 185, indicating its critical role in stabilization. The role of docking in biological activities was recorded to explore the development of active compounds to suppress pathogenic microorganisms, as well as to inhibit the target enzymes responsible for several metabolic activities (Alsalamah et al. 2023; Le Thanh et al. 2023; Binsaleh et al. 2025).

Table 6. Docking Scores and Energies of Sodium Silicate with Structure of Pectin Lyase (PDB ID: 1IDJ), Pectin Methyltranseliminase (PDB ID: 3OQB), and Polygalacturonase (PDB ID: 1K5C)

Table 7. Interaction of Sodium Silicate with Structure of Pectin Lyase (PDB ID: 1IDJ), Pectin Methyltranseliminase (PDB ID: 3OQB), and Polygalacturonase (PDB ID: 1K5C)

2D and 3D diagrams show the interaction between sodium silicate and active sites of Pectin Lyase 1IDJ protein

2D and 3D diagrams show the interaction between sodium silicate and active sites of pectin methyltranseliminase 3OQB protein

2D and 3D diagrams show the interaction between sodium silicate and active sites of Polygalacturonase 1K5C protein

The representative key for the types of interaction between sodium silicate and selected protein receptors

Fig. 1. Interaction between sodium silicate and active sites of enzymes

CONCLUSIONS

1. Sodium silicate showed inhibitor activity on A. flavus growth and their cell wall degrading enzymes.
2. The inhibitor activity of sodium silicate depending on their concentration and period of fungus incubation
3. The molecular docking interaction demonstrated the activity of sodium silicate on the studied cell wall degrading enzymes

ACKNOWLEDGMENTS

The authors would like to acknowledge Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2025R217), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.

FUNDING

This research was funded by Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2025R217), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia

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Article submitted: January 5, 2025; Peer review completed: March 22, 2025; Revised version received and accepted: March 25, 2025; Published: April 9, 2025.

DOI: 10.15376/biores.20.2.3996-4008