2026 Jan; 3(1): 53-74. |
ISSN: 3005-6632 |
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2026 Jan; 3(1): 53-74. |
ISSN: 3005-6632 |
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Abdullah Ahmadzai, Fahim Amirkhezi, *Abdul Musawer Bayan, Muhammad Qadar Adel2, Abdullah Sahar3, Mohammad Reza Mowahhed1, Ehsanullah Rasoly, Rafiullah Shirzadi, Mohammad Ehsanullah Noorkhail
Received: 11 Oct, 2025 Accepted: 28 Dec, 2025 *Corresponding Author: E-mails: Ahmadzai A, Amirkhezi F, Bayan AM, Adel MQ, Sahar A, Mowahhed MR, Rasoly E, Shir-zadi R, Noorkhail ME. Mechanistic Insights from Docking and Dynamics: Soy Isoflavonoids Disrupt P. Aeruginosa Quorum Sensing by Targeting AHL Synthase LasI. Afghanistan Journal of Basic Medical Sciences. 2026 Jan; 3(1): 53-74. DOI: |
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Copyright © 2026 Afghanistan Journal of Basic Medical Sciences, and
Khatam Al-Nabieen University. All rights reserved.
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 International License
The growing crisis of antimicrobial resistance (AMR) is one of the
greatest challenges facing public health in the 21st century (1). This
problem is exemplified by opportunistic pathogens such as
A biofilm consists of a structured community of bacterial cells
embedded in a self-secreted matrix of extracellular polymeric substances
(EPS), comprising polysaccharides, proteins, and extracellular DNA (7).
As a result, biofilm-based infections are extremely resistant to
eradication, with attendant high levels of morbidity, mortality, and
health care costs (8, 9). The inability of traditional antibiotics to
adequately access and eliminate biofilm communities has generated a
compelling need for therapeutic modalities operating by a mode other
than the traditional bactericidal one (9-11). Quorum sensing (QS)
enables the bacterial population to detect the local cell density and
change gene expression coordinately as a population (12). This process
occurs via the production, release, and perception of small diffusible
signals, the autoinducers (13). As the population grows, the level of
the autoinducers builds up in the environment (14).
Soybean isoflavonoids, including genistein, daidzein, and glycitein, come into strong focus as promising lead molecules (19). These natural compounds are not only highly abundant and safe for human consumption but also possess a wide spectrum of documented medical benefits (20). The primary soybean isoflavones such as genistein, daidzein, and glycitein have been extensively studied for their therapeutic potential (21). Genistein is renowned for its potent antioxidant (22), anticancer (23), and phytoestrogenic activities (24). It has been investigated for its role in mitigating menopausal symptoms (25), preventing osteoporosis by modulating bone metabolism (26), and inhibiting the proliferation of various cancer cells (27, 28), particularly in breast and prostate cancer. Daidzein shares similar benefits, including cardioprotective effects through the improvement of lipid profiles and vascular function (29, 30). It is notably metabolized by gut microbiota to equol, a compound with even stronger estrogenic and antioxidant activities (29, 31). Glycitein, while less studied, also exhibits estrogenic properties and has shown neuroprotective and anti-diabetic potential in preclinical models (32-36). Crucially, nascent evidence also suggests intrinsic against a variety of pathogens (37-39).
Yet, against these promising associations, a vital gap persists: the exact, atomistic mechanism by which these isoflavonoids interact and inhibit the synthase LasI enzyme remains completely unstudied. Determining whether they operate as competitive inhibitors, allosteric modulators, or broader structural destabilization is cardinal for their rational development into effective and selective therapeutic agents.
To close this gap, we utilized a computational technique such as molecular docking and molecular dynamic simulation for the study of molecular interaction between the synthase LasI and the soy isoflavonoids.
The structure of
To Interrogate the interactions and binding affinity between genistein, daidzein, or glycitein and synthase LasI (1RO5), we employed a docking technique using Autodock 4.2.2 (42). Proteins structures initially prepared for docking by removing water molecules and co-crystal ligands existed in pdb files and hydrogen atoms with Gasteiger charges added to the system. Subsequently, before proceeding docking method, energy minimization of proteins preformed utilizing GROMACS 2019.6 package using AMBER99SB force field (43). The active sites of proteins were determined by co-crystal ligand reported in pdb file of proteins and then the grid box with the dimensions of 60×60×60 points and a grid point spacing of 0.375 Å was selected. Eventually, 200 docking calculations consisted of the 25 million energy evaluations by using Lamarckian genetic algorithm (LGA) method were performed. Finally, the lowest binding energy conformation in the maximum populated cluster was chosen as the best docking pose and used for molecular dynamic simulation input files.
Investigation of complexes between genistein, daidzein, or glycitein and 1RO5 carried out applying MD simulation technique with more details. MD simulation performed for the three proteins in the free form and in complex with genistein, daidzein, and glycitein in a cubic box solvated by water tip3p model, by GROMACS 2019.6 program using the AMBER99SB force field executed on Kubuntu 2020.4 LINUX operating system, parameters for genistein, daidzein, or glycitein were generated using the Pythonbased ACPYPE tool (AnteChamber Python Parser Interface) (44). Enough number of Na+ or Cl- ions were added to neutralize system charges and achieve to the physiological ion concentration of 0.15 M. In the first step rapid descend method utilized for energy minimization process. Then energy minimized systems were balanced with 1ns simulations in nvt and not ensembles in 310 K and 1 bar. After the systems were well balanced, MD run was performed with a time step of 2 fs for 200 ns simulation time. Eventually, simulated trajectories were used to study the molecular structure of protein, ligand and intermolecular interactions during the simulation time. For analysis purposes, plots for root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA), along with hydrogen bond analysis, were generated and analysed.
Molecular docking analysis demonstrated that the isoflavonoids genistein, daidzein, and glycitein exhibit strong binding affinity for the synthase LasI, with daidzein showing the most potent inhibition potential (ΔG = -7.90 kcal/mol; Ki = 1.62 µM), closely followed by glycitein (ΔG = -7.82 kcal/mol; Ki= 1.85 µM) and genistein (ΔG = -7.51 kcal/mol; Ki = 3.13 µM), as shown in Table 1. The high number of conformations in the top-ranked clusters (Genistein: 198; Daidzein: 200; Glycitein: 128) indicates a stable and reliable binding pose for each complex. The all complexes (Fig. 1a, 1b and 1c) revealed a multifaceted interaction network involving key residues Arg30 and Val143. The ligands are stabilized within the binding pocket through hydrogen bonds interactions with Arg30 and Val143.
In the Synthase LasI/Genistein complex (Fig. 1a), distinct binding patterns emerged with hydrogen bonds between: Genistein's carbonyl group and Arg30 (2.64 Å); and its hydroxyl group with Val143 (2.76 Å). These variations highlight Genistein's structural flexibility in accommodating different enzyme microenvironments. Similarly, the Synthase LasI/Daidzein complex (Fig. 1b), also shows hydrogen bonds interactions between: Daidzein's carbonyl group and Arg30 (2.64 Å); and its hydroxyl group with Val143 (2.76 Å). The Synthase LasI/Glycitein (Fig. 1c), also follow the above interaction hydrogen bonds pattern, in which the glycitein maintained a hydrogen bond with carbonyl group of Arg30 (2.63 Å) and hydroxyl group of Val143 (2.68 Å). Comparative analysis of the three complexes reveals a conserved interaction with a critical cluster of residues, including Arg30 and Val143. This suggests a shared binding region and a common inhibition mechanism despite the subtle structural differences between the isoflavonoids. The variations in the precise interaction networks explain the differences in their binding energies and inhibitory constants.
These findings collectively suggest that isoflavonoids, particularly daidzein and glycitein, possess significant potential as inhibitors of synthase LasI. The conserved interactions with key hydrophobic and polar residues provide a robust structural foundation for developing optimized synthase LasI inhibitors through targeted medicinal chemistry approaches aimed at enhancing these critical contacts.
| Cluster rank | 1 | 1 | 1 |
| Number in cluster | 198 | 200 | 128 |
| Lowest Binding Energy (kcal/mol) | -7.51 | -7.90 | -7.82 |
| 3.13 | 1.62 | 1.85 |
To corroborate and expand upon our molecular docking results, we conducted extensive 200 ns molecular dynamics (MD) simulations for the Synthase LasI enzyme in both its unbound state and complexed with each isoflavonoid ligand (genistein, daidzein, and glycitein). These simulations were essential to assess the stability of the complexes and monitor the temporal evolution of protein-ligand interactions under conditions mimicking the physiological environment.
Our investigation centered on several critical metrics that offer insights into the system’s behavior: 1) root mean square deviation (RMSD) to evaluate structural steadiness, 2) root mean square fluctuation (RMSF) to probe per-residue flexibility, 3) radius of gyration (Rg) to measure overall compactness, 4) solvent accessible surface area (SASA) to determine surface exposure changes, and 5) hydrogen bond formation patterns to characterize interaction persistence. Furthermore, we applied the molecular mechanics Poisson–Boltzmann surface area (MMPBSA) method to compute binding free energies and identify the principal thermodynamic components stabilizing the complexes.
RMSD analysis The RMSD analysis (Fig. 2) revealed distinct stabilization profiles for each Synthase LasI system, providing crucial insights into the differential effects of isoflavonoid binding on the enzyme's dynamic stability. A detailed examination of the trajectories shows significant variations in the time required for each system to reach equilibrium.
For the Synthase LasI/Genistein complex (Fig. 2a), a marked difference in equilibration kinetics was observed. The bound form reached a stable equilibrium significantly earlier, at approximately 120 ns, and maintained a consistently lower fluctuation profile throughout the simulation. In stark contrast, the apo form required a longer duration, stabilizing only at approximately 160 ns. This earlier equilibration and the complex's final lower mean RMSD of 0.169 ± 0.011 nm (compared to the apo's 0.202 ± 0.019 nm, Table 2) indicate that Genistein binding not only enhances the structural stability of the enzyme but also accelerates the convergence to a stable conformational state. This profile suggests Genistein acts primarily through a competitive inhibition mechanism. It likely binds directly to the enzyme's active site with high affinity, forming a stable complex that restricts essential conformational motions and prevents the native substrate from binding.
The Synthase LasI/Daidzein complex (Fig. 2b) exhibited a different behavior. In this case, both the apo and bound forms reached equilibrium at approximately the same time, around 160 ns. Post-equilibration, the bound form showed a marginally higher final mean RMSD (0.209 ± 0.030 nm) compared to the free enzyme (0.202 ± 0.019 nm). The increased average further suggests greater residual flexibility within the complex. This implies that while Daidzein binds with the highest affinity (as per docking results, Table 1), its binding mode does not hasten structural stabilization and may induce major conformational dynamics or flexibility in the enzyme structure. This dynamic profile is not typical of a classic competitive inhibitor. Instead, it suggests Daidzein may function through an allosteric mechanism
The Synthase LasI/Glycitein system (Fig. 2c) displayed the most pronounced effect on equilibration kinetics. The bound form reached equilibrium remarkably quickly, at approximately 80 ns, demonstrating a rapid and stable binding event. Meanwhile, the apo form required a full 160 ns to stabilize. This dramatically faster equilibration, coupled with a final mean RMSD (0.195 ± 0.022 nm) that is nearly identical to the apo form's (0.202 ± 0.019 nm), indicates that Glycitein binding induces minimal perturbation to the enzyme's global backbone structure while profoundly accelerating its transition to a stable conformational state. This suggests a highly complementary and stabilizing fit, consistent with an efficient competitive inhibition mechanism.
These findings collectively illustrate the nuanced impact of each isoflavonoid on Synthase LasI's dynamics. Genistein and Glycitein significantly accelerate the enzyme's transition to a stable state while enhancing or maintaining structural rigidity, respectively. Daidzein highest binding affinity, may act as an allosteric inhibition, subtly altering the enzyme's dynamics with enhanced flexibility and disruption the functionality and structural integrity of the Synthase LasI.
| Free Synthase LasI | 0.202 ± 0.019 | 1.626 ± 0.011 | 0.116 ± 0.051 | 103.952 ± 2.330 |
| Synthase LasI/ Genistein | 0.169 ± 0.011 | 1.629 ± 0.006 | 0.098 ± 0.052 | 104.46 ± 1.976 |
| Synthase LasI/ Daidzein | 0.209 ± 0.030 | 1.634 ± 0.009 | 0.124 ± 0.088 | 105.78 ± 2.347 |
| Synthase LasI/ Glycitein | 0.195 ± 0.022 | 1.615 ± 0.008 | 0.102 ± 0.051 | 102.79 ± 2.255 |
Complementing the RMSD findings, Rg measurements provided essential insights into the tertiary structural alterations induced by isoflavonoid binding in the Synthase LasI systems. The Rg parameter, which quantifies the spatial distribution of atomic mass relative to the protein’s center of mass, serves as a sensitive indicator of global structural compaction or expansion. Analysis of the Rg trajectories (Fig. 3) revealed distinct ligand-specific structural responses that align closely with the RMSD profiles.
For the Synthase LasI/Genistein complex, Rg values exhibited minimal deviation upon ligand binding. The complexed form demonstrated a mean Rg of 1.629 ± 0.006 nm, nearly identical to the apo form (1.626 ± 0.011 nm) during the production phase (last 50 ns, Table 2). This consistency suggests that Genistein binding enhances structural stability without perturbing the overall tertiary architecture, supporting a binding mode that complements the native enzyme conformation.
In the Synthase LasI/Daidzein complex, a slight increase in Rg was observed, with the bound state measuring 1.634 ± 0.009 nm compared to 1.626 ± 0.011 nm for the unbound enzyme. This marginal expansion correlates with previously noted increases in structural flexibility (RMSD), indicating that Daidzein binding may induce a de compaction of the tertiary structure, potentially enhancing conformational dynamics.
Conversely, the Synthase LasI/Glycitein complex exhibited a pronounced compaction, with the bound form yielding an Rg of 1.615 ± 0.008 nm—significantly lower than that of the free enzyme (1.626 ± 0.011 nm). This reduction in Rg signifies enhanced global compactness and structural rigidity, consistent with the rapid equilibration and reduced fluctuations observed in RMSD analysis. This suggests that Glycitein binding promotes a more condensed and stable tertiary conformation. Temporal analysis of the Rg trajectory for Glycitein (Fig. 3c) indicates that this compaction is rapidly established and sustained throughout the simulation, aligning with its swift RMSD stabilization. This suggests an immediate and sustained effect on the enzyme’s structural ensemble, leading to a more ordered and compact state.
Collectively, these Rg results elucidate the diverse structural impacts of isoflavonoid binding: Genistein preserves native compactness, Daidzein induces expansion, and Glycitein significantly enhances global compaction. These findings highlight the role of ligand-specific interactions in modulating the structural plasticity and thermodynamic stability of Synthase LasI, underpinning their potential as distinct mechanistic inhibitors.
The RMSF results for Synthase LasI show that while the core structural elements of the enzyme remain relatively stable, specific loops and terminal regions display significant flexibility. In its free state, the enzyme exhibits the greatest movement in regions associated with binding and solvent interaction, a characteristic that makes biological sense for facilitating ligand binding and molecular recognition. In contrast, the putative catalytic and structural core regions remain quite rigid, which is essential for maintaining the enzyme's precise functional geometry.
Upon ligand binding, we see consistent but distinct reductions in flexibility across the three complexes, with the most noticeable effects occurring in key regions. The more distant N- and C-terminal regions of the enzymes largely retain their flexibility, showing that the ligands' effects are localized to the binding pocket and its adjacent loops rather than causing widespread changes to the entire enzyme structure. Together, these observations suggest that the isoflavonoids work by subtly limiting the natural movement of specific loops, potentially those involved in substrate recruitment or binding, rather than causing major structural rearrangements.
Looking at each complex individually, the Synthase LasI/Genistein complex (Fig. 4a) demonstrates the most pronounced stabilizing effect. This is quantified by its significantly lower mean RMSF value (0.098 ± 0.052 nm) compared to the free enzyme (0.116 ± 0.051 nm). Genistein binding results in a widespread suppression of fluctuations across multiple residue ranges, particularly in the regions between residues 20-80 and 100-170. This strong reduction in flexibility indicates that Genistein forms extensive interactions that effectively dampen the intrinsic dynamics of the enzyme, locking it into a more rigid and stable conformation.
The Synthase LasI/Daidzein complex (Fig. 4b) presents a contrasting profile. The bound system shows a marginally higher mean RMSF (0.124 ± 0.088 nm) than the free enzyme. The RMSF trajectory indicates that while some regions become slightly more stable, others, particularly around residues 20-40 and 80-100 and the C-terminal region, exhibit increased fluctuations. This suggests that Daidzein binding does not uniformly stabilize the structure but may induce a degree of dynamic flexibility or allosteric rearrangement in specific loops, correlating with its observed higher RMSD and Rg. The Synthase LasI/Glycitein complex (Fig. 4c) shows a focused and effective stabilization. The mean RMSF (0.102 ± 0.051 nm) is lower than that of the apo enzyme, indicating an overall reduction in flexibility.
Although the changes in flexibility vary in magnitude and nature, the fact that they consistently occur in specific regions suggests a common theme of targeted dynamic modulation. The isoflavonoids appear to function by selectively restricting the natural flexibility of loops that are crucial for enzyme function. By reducing these motions, the ligands likely impede the conformational changes necessary for substrate binding or catalysis, even though they do not dramatically alter the enzyme's overall fold. Genistein and Glycitein acts as a global stabilizer, and Daidzein may introduce specific flexibility that could be linked to an alternative inhibitory mechanism.
The analysis of the SASA trajectories (Fig. 5) and their averaged values (Table 2) provides a crucial dimension to our understanding of the structural dynamics induced by isoflavonoid binding, revealing how each ligand uniquely modulates the enzyme's interaction with its aqueous environment.
Fig. 5a (Synthase LasI/Genistein) shows a SASA trajectory for the complex that is remarkably congruent with the apo enzyme throughout the entire 200 ns simulation. Both systems reach a stable equilibrium by approximately 130 ns and maintain a consistent oscillation around nearly identical mean values. The plot visually confirms the quantitative data in Table 2, which shows a marginal, statistically insignificant increase in mean SASA for the complex (104.46 ± 1.976 nm²) compared to the apo form (103.952 ± 2.330 nm²). This indicates that Genistein binding achieves its potent stabilizing effect (as seen in low RMSD/RMSF) without perturbing the global solvation surface of the enzyme. This is characteristic of a ligand that binds with high complementarity, stabilizing the internal structure while perfectly preserving the external topological features of the native state.
Fig. 5b (Synthase LasI/Daidzein) presents a distinctly different profile. The trajectory for the complex consistently runs above that of the apo enzyme for the majority of the simulation time, particularly after the 50 ns mark. This visual expansion of the solvent-accessible surface is quantitatively confirmed by the highest mean SASA value of 105.78 ± 2.347 nm² (Table 2). This indicates a greater degree of dynamic flexibility in the bound state. This sustained increase in SASA provides direct visual evidence that Daidzein binding induces a loosening of the tertiary structure, exposing hydrophobic patches to the solvent. This mechanism aligns perfectly with its higher RMSD and Rg values, painting a coherent picture of a more dynamic and expanded complex.
Fig. 5c (Synthase LasI/Glycitein) reveals the most significant visual shift. The trajectory for the complex is clearly and consistently displaced below the apo enzyme's graph for the entire simulation duration after initial equilibration. This pronounced and sustained reduction in solvent-accessible surface is quantitatively robust, with the complex exhibiting the lowest mean SASA value of 102.79 ± 2.255 nm² (Table 2). The plot shows that this compaction is not a transient event but a stable property of the complex. This provides unambiguous evidence that Glycitein binding drives a global compaction of the enzyme structure. This forces a more efficient packing of the protein interior, burying hydrophobic residues and reducing the overall surface area exposed to the solvent. This observation is entirely consistent with Glycitein’s reduction in Rg and its strong, favorable van der Waals energy component (-169.341 ± 9.399 kJ/mol, Table 4), which is the primary driver of its binding. The SASA results complete our multidimensional assessment of Synthase LasI's structural response, showing how the same biological endpoint (enzyme inhibition) can be achieved through different biophysical pathways. This diversity in mechanism may prove advantageous for developing targeted therapies that inhibit Synthase LasI through complementary structural disruptions.
The hydrogen bonding patterns and binding energetics provide critical insights into the molecular interactions stabilizing the Synthase LasI-ligand complexes, revealing distinct mechanistic profiles for each isoflavonoid.
Analysis of the hydrogen bond trajectories (Fig. 6) reveals how ligand binding differentially stabilizes the Synthase LasI system through distinct modifications of its interaction landscape. Throughout the 200 ns simulations, all three ligands formed stable hydrogen bonds with the enzyme. Synthase LasI/Genistein (Fig. 6a) maintained the consistent and extensive network, forming a stable with maximum of 5 hydrogen bonds throughout the simulation time. Synthase LasI/Daidzein (Fig. 6b) exhibited a more dynamic profile, forming maximum number of 6 hydrogen bonds with greater variability, suggesting a binding mode that allows for more flexibility in its polar interactions. Synthase LasI/Glycitein (Fig. 6c) formed a stable but smaller network of 3 hydrogen bonds.
The profound effects of ligand binding are further evident when examining the propagation of these interactions through the enzyme's intramolecular and solvation networks (Fig. 7 and Fig. 8). For the Synthase LasI/Genistein complex, the binding event triggers a significant restructuring of the hydrogen bonding architecture. We observe a slight increase in intramolecular hydrogen bonds (158.912 ± 5.919) compared to the apo form (157.549 ± 5.811), accompanied by a substantial reduction in solvent hydrogen bonds (401.436 ± 12.620 vs 408.388 ± 12.939). This dual effect suggests Genistein binding induces a global structural tightening, where the formation of new internal hydrogen bonds and the ligand's own persistent H-bonds compensate for the displacement of water molecules from the binding site.
The Synthase LasI/Daidzein complex exhibits a different response. It shows a marginal decrease in intramolecular H-bonds (156.001 ± 6.208) and a smaller reduction in solvent H-bonds (406.731 ± 12.972) compared to the apo form. This pattern suggesting that its binding site remains somewhat accessible to water, leading to the greater overall flexibility we saw in the RMSD and Rg analyses. In contrast, the Synthase LasI/Glycitein complex presents a unique case. It shows a significant increase in intramolecular H-bonds (158.775 ± 6.023) alongside a pronounced reduction in solvent H-bonds (390.792 ± 12.112), the largest decrease among all complexes. This indicates that Glycitein binding promotes a dramatic restructuring of the hydrogen bonding network, favoring a more internally bonded, de solvated, and compact structure, which is entirely consistent with its lowest SASA and Rg values.
The MMPBSA calculations (Table 4) quantitatively affirm the stability trends inferred from hydrogen bonding and provide the thermodynamic rationale for the observed structural effects.
Synthase LasI/Genistein emerged as the strongest binder with a binding energy of -188.719 ± 8.675 kJ/mol. This superior affinity is overwhelmingly driven by exceptionally robust van der Waals contributions (-225.231 ± 8.983 kJ/mol), which constitute nearly the entirety of the favorable energy. The minimal electrostatic contribution (-2.906 ± 3.387 kJ/mol) and a moderate polar solvation penalty (52.231 ± 3.614 kJ/mol) indicate a binding mode dominated by shape complementarity and hydrophobic packing, perfectly explaining its strong stabilization without major structural perturbation.
Synthase LasI/Daidzein demonstrated significant but intermediate binding affinity (-118.179 ± 8.564 kJ/mol). Its binding is characterized by a strong van der Waals component (-154.077 ± 9.395 kJ/mol) and a notably more favorable electrostatic energy (-11.408 ± 4.899 kJ/mol) compared to the other ligands, suggesting a greater role for polar interactions. However, this is offset by a higher polar solvation penalty (61.480 ± 5.311 kJ/mol), which moderates its overall binding energy. This energetic profile aligns with its dynamic binding mode, allowing for strong but flexible interactions.
Synthase LasI/Glycitein, while having the least favorable net binding energy (-105.614 ± 10.421 kJ/mol), displays a strong van der Waals component (-169.341 ± 9.399 kJ/mol). Its binding is severely hampered by the largest polar solvation penalty (81.955 ± 8.071 kJ/mol), indicating a significant energetic cost to desolvating the ligand and the binding site. This explains its mechanism: the strong hydrophobic driving force is powerful enough to pay the cost for extensive de solvation and dramatic structural compaction, resulting in the tightly packed complex observed in the Rg and SASA analyses
| Free Synthase LasI | 157.549 ± 5.811 | 408.388 ± 12.939 |
| Synthase LasI/ Genistein | 158.912 ± 5.919 | 401.436 ± 12.620 |
| Synthase LasI/ Daidzein | 156.001 ± 6.208 | 406.731 ± 12.972 |
| Synthase LasI/ Glycitein | 158.775 ± 6.023 | 390.792 ± 12.112 |
| van der Waal energy | -225.231+/-8.983 | -154.077+/-9.395 | -169.341+/-9.399 |
| Electrostatic energy | -2.906+/-3.387 | -11.408+/-4.899 | -2.683+/-3.678 |
| Polar solvation energy | 52.231+/-3.614 | 61.480+/-5.311 | 81.955+/-8.071 |
| SASA energy | -12.813+/-0.633 | -14.174+/-0.706 | -15.546+/-0.772 |
| Binding energy | -188.719+/-8.675 | -118.179+/-8.564 | -105.614+/-10.421 |
This computational study reveals that soy isoflavonoids, particularly
genistein, daidzein, and glycitein, exhibit distinct inhibitory profiles
against the
When compared to recent literature, these findings find strong validation, intriguing contrasts, and open new avenues for the rational design of QS inhibitors. Our molecular docking analysis, which identified Arg30 and Val143 as critical for isoflavonoid binding, is strongly corroborated by mechanistic studies on synthetic inhibitors. Research on the thiazolidinedione derivative TZD-C8, a potent LasI inhibitor, utilized in silico docking and site-directed mutagenesis to conclusively demonstrate that residues Arg30 and Ile107 are essential for its inhibitory activity (45, 46). The abolition of TZD-C8's effect in a LasI double mutant (R30D, I107S) provides robust experimental validation for targeting this region of the enzyme's active site. This parallel underscores the reliability of our computational approach in predicting functionally relevant interactions and highlights Arg30 as a conserved hotspot for inhibitor design, whether the scaffolds are synthetic or natural.
While our study and the work on TZD-C8 focus on direct competitive
binding to the synthase's active site, other research illustrates the
diverse mechanisms by which natural products can disrupt QS circuitry. A
study on the natural chalcone isoliquiritigenin demonstrated potent
anti-virulence effects against
Our molecular dynamics simulations suggested that daidzein may induce a degree of conformational flexibility in LasI, hinting at a potential allosteric or dynamic mode of inhibition. This concept is supported by pioneering work on the related synthase RhlI. Research on acyl-homoserine lactone (AHL) analogs targeting RhlI revealed the existence of two distinct binding pockets one for inhibitors and another for activators within the enzyme (48, 49). This discovery of allosteric sites in a LuxI-type synthase provides a plausible structural basis for the dynamic effects we observed with daidzein. It raises the compelling hypothesis that certain isoflavonoids might not only compete at the active site but also bind to secondary, regulatory pockets to modulate enzyme activity, a possibility meriting further investigation. The ultimate goal of anti-virulence strategies is to attenuate infection without promoting resistance. Both our findings and the broader literature affirm this promise. For instance, isoliquiritigenin was reported to develop no resistance over 20 generations and, crucially, to increase the sensitivity of P. aeruginosa to aminoglycoside antibiotics like tobramycin and amikacin (47, 50). This aligns perfectly with the strategic rationale for QS inhibition: by disarming the bacteria's virulence apparatus, these compounds can render pathogens more susceptible to host immune clearance and enhance the efficacy of conventional antibiotics, creating a powerful synergistic therapeutic approach.
Natural isoflavonoids, particularly genistein, can effectively target
and stabilize the quorum-sensing synthase LasI in
The authors declare that they have no competing interests.
This research was supported by resources supplied by the deputy of financial affairs of the Ghalib University, Kabul, Afghanistan.
The authors would like to express their utmost gratitude to the Board of Directors of Ghalib University, Kabul, Afghanistan for support and motivations, especially Dr. M. I. Noori and Eng. A. Ahadi. Special thanks to Mr. Mohammad Yousoof Saleh (Head of HR and financial affairs of Ghalib University) and his team, for assisting us in better performance of this study.
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