Molecular Docking of Nimbolide Extracted from Leaves of Azadirachta indica with Protein Targets to Confirm the Antifungal, Antibacterial and Insecticidal Activity

Nimbolide, a tetranortriterpenoid (limonoid) compound isolated from the leaves of Azadirachta indica, was screened both in vitro and in silico for its antimicrobial activity against Fusarium oxysporum f. sp. cubense, Macrophomina phaseolina, Pythium aphanidermatum, Xanthomonas oryzae pv. oryzae, and insecticidal activity against Plutella xylostella. Nimbolide exhibited a concentration-dependent, broad spectrum of antimicrobial and insecticidal activity. P. aphanidermatum (82.77%) was more highly inhibited than F. oxysporum f. sp. cubense (64.46%) and M. phaseolina (43.33%). The bacterium X. oryzae pv. oryzae forms an inhibition zone of about 20.20 mm, and P. xylostella showed about 66.66% mortality against nimbolide. The affinity of nimbolide for different protein targets in bacteria, fungi, and insects was validated by in silico approaches. The 3D structure of chosen protein molecules was built by homology modelling in the SWISS-MODEL server, and molecular docking was performed with the SwissDock server. Docking of homology-modelled protein structures shows most of the chosen target proteins have a higher affinity for the furan ring of nimbolide. Additionally, the stability of the best-docked protein-ligand complex was confirmed using molecular dynamic simulation. Thus, the present in vitro and in silico studies confirm the bioactivity of nimbolide and provide a strong basis for the formulation of nimbolide-based biological pesticides.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01104-6.

Triamcinolone Acetonide Produced by Bacillus velezensis YEBBR6 Exerts Antagonistic Activity Against Fusarium oxysporum f. sp. Cubense: A Computational Analysis

Fusarium oxysporum f. sp. cubense is one of the most severe and threatening pathogens of bananas, causing "Panama wilt" worldwide. Confrontation assay of Foc antagonistic bacterial endophyte, Bacillus velezensis YEBBR6, with the Foc and GC-MS profiling of excised agar from the zone of inhibition, led to the unveiling of secondary metabolites produced by the endophyte. To refine the probable antifungal compounds among the numerous biomolecules formed during their di-trophic interaction with the pathogen, fungal protein targets were modeled, and docking studies (AutoDock Vina module of the PyRx 0.8 server) were done with all the compounds. Triamcinolone acetonide exhibited the most excellent affinity for the protein targets among the compounds studied. It had a maximum binding affinity of 11.2 kcal/mol for XRN2 (5' → 3'). Further, the protein-ligand complex formation kinetics was done through Molecular Dynamic Simulation studies. Graphs for the RMSD, RMSF, Rg, potential energy, and SASA were generated, and the values during the simulation period suggested the stability of the biomolecule as a complex with the protein. This indicated Triamcinolone acetonide's potential ability to act as a functional disrupter of the target protein and likely an antifungal molecule. Further, the biomolecule was tested for its activity against Foc by screening in the wet lab through the poisoned plate technique, and it was found to be fully inhibitory to the growth of the pathogen at 1000 ppm.

Synthesis, characterization, reaction mechanism prediction and biological study of mono, bis and tetrakis pyrazole derivatives against Fusarium oxysporum f. sp. Albedinis with conceptual DFT and ligand-protein docking studies

Twelve heterocyclic compounds were prepared using the condensation of hydroxymethanol pyrazole derivatives with different primary aminesas example 2-aminothiazole and 1-aminobenzotriazole to have a diverse productin good yield up to 97%. Those ligands were tested against Fusarium oxysporum f. sp. Albedinis fungi (BAYOUD Disease) with IC₅₀ = 25.6-33.2 µg/ml. After experiments, theoretical investigations were done as DFT study to know the ligands molecular reactivity and the-ligandprotein- docking study to know the possible binding between the prepared ligands with two biological targets: FGB1 (Fusarium oxysporum Guanine nucleotide-binding protein beta subunitprimary amino acid sequence) and Fophy (Fusarium oxysporum phytase domain enzyme). Of all the obtained results, the experimental ones were well correlated with the theoretical with the most common thing between those compounds is (N^δ--N^δ+) which is the antifungal pharmacophore as proposed pincers for Foa inhibition. From docking studies over FGB1 and Fophy, the ligand 9 has the best binding energy of -6.4872 kcal/mol in FGB1 active site and -5.5282 kcal/mol in Fophy active site, but better correlation with Fophy than FGB1 which is followed by PLIF graph to get that Arg116, Arg120 and Lys336 are the vital amino acids of fophy protein based the study over the chosen active site.

Mono-Alkylated Ligands Based on Pyrazole and Triazole Derivatives Tested Against Fusarium oxysporum f. sp. albedinis: Synthesis, Characterization, DFT, and Phytase Binding Site Identification Using Blind Docking/Virtual Screening for Potent Fophy Inhibitors

Twelve recent compounds, incorporating several heterocyclic moieties such as pyrazole, thiazole, triazole, and benzotriazole, made in excellent yield up to 37–99.6%. They were tested against Fusarium oxysporum f. sp. albedinis fungi (Bayoud disease), where the best results are for compounds 2, 4, and 5 with IC₅₀ = 18.8–54.4 μg/mL. Density functional theory (DFT) study presented their molecular reactivity, while the docking simulations to describe the synergies between the trained compounds of dataset containing all the tested compounds (57 molecules) and F. oxysporum phytase domain (Fophy) enzyme as biological target. By comparing the results of the docking studies for the Fophy protein, it is found that compound 5 has the best affinity followed by compounds 2 and 4, so there is good agreement with the experimental results where their IC₅₀ values are in the following order: 74.28 (5) < 150 (2) < 214.10 (4), using Blind docking/virtual screening of the homology modeled protein and two different tools as Autodock Vina and Dockthor web tool that gave us predicted sites for further antifungal drug design.

Synthesis, Antimicrobial Screening, Homology Modeling, and Molecular Docking Studies of a New Series of Schiff Base Derivatives as Prospective Fungal Inhibitor Candidates

Twelve new Schiff base derivatives have been prepared by the condensation reaction of different amino substituted compounds (aniline, pyridin-2-amine, o-toluidine, 2-nitrobenzenamine, 4-aminophenol, and 3-aminopropanol) and substituted aldehydes such as nicotinaldehyde, o,m,p-nitrobenzaldehyde, and picolinaldehyde in ethanol using acetic acid as a catalyst. The envisaged structures of the all the synthesized ligands have been confirmed on the basis of their spectral analysis FT-IR, mass spectroscopy, ¹H- and ¹³C-NMR. In vitro screening of their antibacterial and antifungal potential against Escherichia coli bacterium and Fusarium oxysporum f.sp albedinis (F.o.a) fungus, respectively, revealed that all the ligands showed no significant antibacterial activity, whereas most of them displayed good antifungal activity. Homology modeling and docking analysis were performed to explain the antifungal effect of the most and least active compound against two F.o.a fungus proteins.

In vitro screening, homology modeling and molecular docking studies of some pyrazole and imidazole derivatives

A series of synthesized compounds based on pyrazole and imidazole skeletons prepared by palladium catalysts via a one-pot reaction was screened to determine their inhibitory potency against the pathogen fungus Fusarium oxysporum f.sp. albedinis (F.o.a) and four bacteria strains namely Micrococcus luteus, Bacillus subtilis, Staphylococcus aureus and Escherichia coli. The obtained result showed that these compounds exhibit an efficiency antifungal action. Whereas, they showed a very weak antibacterial activity. The structure-activity relationship (SAR) Analysis and lipophilicity study demonstrates the presence of a strong relation between the structure of the ligands and the antifungal activity. On the other hand, a homology modeling and molecular docking study was carried out on the most active compounds against F.o.a fungus, in order to understand and determine the molecular interactions taking place between the ligand and the corresponding receptor of the studied target.

Computer-Aided Drug Discovery in Plant Pathology

Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.