In Silico Approach Targeting Polyphenol as Fabh Inhibitor in Bacterial Infection

Dhawale, Sachin A; Gawale, Sachin; JADHAV, AKASH; GETHE, KALYANI; RAUT, PRASHANT; HIWARALE, NIKITA; BHOSALE, PALLAVI; Tapadiya, Ganesh G.

doi:10.22159/ijpps.2022v14i11.45816

Cited by 7 publications

(3 citation statements)

References 24 publications

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“…5BNR protein was obtained from RCSB which was a bacterial protein obtained from E. coli bacterial organism with mutant E. coli K‐12 and classified under Transferase inhibitor, 3QCP was a bacterial protein again obtained from E. coli from organism Trypanosoma brucei which was classified under oxidoreductase enzyme. Bacterial protein 1AI9 was obtained from Candida albicans and classified under oxidoreductase type 34 …”

Section: Methodsmentioning

confidence: 99%

Green synthesis of silver nanoparticles mediated Azadirachta indica extract and study of their characterization, molecular docking, and antibacterial activity

Gawai,

Kharat,

Chorge

et al. 2023

J of Molecular Recognition

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The green production of silver nanoparticles (AgNPs) produces AgNPs with minimum influence on the environment by using plant components such as alkaloids, carbohydrates, lipids, enzymes, flavonoids, terpenoids, and polyphenols as reducing agents. In the present investigation, Azadirachta indica leaf extract was used to form AgNPs from a 1 mM silver nitrate solution. The plan proved to be incredibly straightforward, cost‐effective, and effective. The production of the nanoparticles was observed visually, where the colorless fluid turns into a brown‐colored solution. Further research was carried out using x‐ray diffraction, Fourier‐transform infrared analysis, scanning electron microscopy, and transmission electron microscopy (TEM) in addition to UV–visible spectroscopy. The size range of AgNPs determined by TEM was 10–30 nm. When the diffusion technique was employed to demonstrate the antibacterial effect of AgNPs on various pathogens, the zones of inhibition for Staphylococcus aureus, Bacillus cereus, and Escherichia coli, when 50 g of AgNPs were used were 16, 12, and 17 mm, respectively. By examining the leakage of reducing sugars and proteins, the mechanism by which nanoparticle antibacterial properties were explored, showed that AgNPs were capable of lowering membrane permeability.

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Section: Methodsmentioning

confidence: 99%

Green synthesis of silver nanoparticles mediated Azadirachta indica extract and study of their characterization, molecular docking, and antibacterial activity

Gawai,

Kharat,

Chorge

et al. 2023

J of Molecular Recognition

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show abstract

“…An OPLS3e force field with a VSGB 2.0 solvation model was used for energy minimization [16]. This technique contains optimal implicit solvation for hydrogen bonding, self-contact interactions, and hydrophobic interactions, in addition to a physics-based correction [17].…”

Section: Binding Free Energy Calculations Using Prime Mm-gbsamentioning

confidence: 99%

Design for the Colon Cancer Inhibitors Targeting Thymidylate Kinase by Using Insilico Studies

BAQI,

JAYANTHI,

RAJESHKUMAR

2024

Int J App Pharm

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Objective: Thymidylate Kinase (TMK) plays a crucial role in bacterial DNA synthesis by catalyzing the phosphorylation of Deoxythymidine Monophosphate (dTMP) to form Deoxythymidine Diphosphate (dTDP). Consequently, this enzyme emerges as a promising target for developing novel anti-cancer drugs. However, no anti-cancer drugs have been reported for this target until now. Methods: Ligands obtained from Benzylidene derivatives were examined for their potency by using molecular docking by glide module, Qikprop screening of Absorption, Distribution, Metabolism, and Excretion (ADME) study, and prime Molecular Mechanics in Generalized Bond Surface Area study (MM-GBSA) by binding free energy. Hereafter, a Molecular Dynamic (MD) simulation was performed at 100 ns to assess the stability of the potential ligand as a Human TMK (HaTMK) inhibitor. Results: These ten molecules showed good binding affinity and hydrogen and hydrophobic bond interactions with Arg150, Phe42, and Phe72 in the HaTMK enzyme (PDB id: 1E2D). Among them, trichloro-6-(((4-hydroxyphenyl)imino)methyl)phenol molecule had a high XP-docking score of (−7.87 kcal/mol), based on extra-precision data. Prime MM-GBSA studies also showed promising binding affinities i.e., ΔBind (-34.59 kcal/mol), ΔLipo (-13.92 kcal/mol), and ΔVdW (-34.42 kcal/mol). Arg76 and Phe72 residues maintained constant interactions with the ligand during Molecular Dynamics (MD) simulation. This ligand showed a potential binding affinity for the TMK target. Conclusion: The trichloro-6-(((4-hydroxyphenyl)imino)methyl)phenol ligand has active sites, namely benzene ring, benzylidene, and oxygen group, which actively participate in interaction with the protein of HaTMK, thus indicating good potential activity as the inhibitor of HaTMK to treat colon cancer.

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“…The binding free energy for each protein-ligand combination was calculated using the prime Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) approach (Schrödinger suite 2019-2). An OPLS3e force field with a VSGB 2.0 solvation model was used for energy minimization [21,22]. This technique contains optimal implicit solvation for hydrogen bonding, self-contact interaction interactions, and hydrophobic interactions, in addition to a physicsbased correction.…”

Section: Binding Free Energy Calculations Using Prime Mm-gbsamentioning

confidence: 99%

Molecular Docking Dynamics of Selected Benzylidene Amino Phenyl Acetamides as TMK Inhibitors Using High Throughput Virtual Screening (Htvs)

JAYANTHI,

AHMED,

BAQI

et al. 2024

Int J App Pharm

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Objective: Thymidylate kinase (TMK) plays a crucial role in bacterial DNA synthesis by catalyzing the phosphorylation of deoxythymidine monophosphate (dTMP) to form deoxythymidine diphosphate (dTDP). Consequently, this enzyme emerges as a promising target for developing novel antibacterial drugs. However, no antibiotics were reported for this target, especially active against Staphylococcus aureus thymidylate kinase. Methods: Benzylidene acetamide-based ligands were examined for their potency using the in silico method. These novel ligand structures were built using ChemDraw software. The protein was retrieved from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) website. The molecular docking and binding free energy calculation by prime Molecular Mechanics in Generalized Bond Surface Area (MM-GBSA) was performed for selected ligands. A 100 ns molecular dynamic simulation was also performed to assess the stability of the potential ligand as TMK inhibitors. Results: All ten molecules have shown good glide scores and hydrophobic and hydrogen hydrophobic hydrogen bonding interactions with Arg48, Arg36, and π-π stacking Phe66 in the TMK enzyme (PDB: 4HLC). Among them, N-(2-ethylphenyl)-2-(4-((4-nitrobenzylidene) amino) phenoxy) acetamide molecule had high XP-docking scores of-3.27 kcal/mol based on extra-precision data. Prime Molecular Mechanics in Generalized Bond Surface Area study (MM-GBSA) studies also showed promising binding affinities that are ΔBind (-65.80), ΔLipo (-28.55), and ΔVdW (-55.10). Phe66 amino acid residue maintained continuous connections with the ligand during MD simulation. This ligand showed promising binding affinity with the SaTMK target. Conclusion: The N-(2-ethylphenyl)-2-(4-((4-nitrobenzylidene) amino) phenoxy) acetamide ligand at the position of the benzene ring displayed nitrogen and oxygen group, thus indicating good potential activity as the inhibitor of TMK to treat antibacterial agents.

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In Silico Approach Targeting Polyphenol as Fabh Inhibitor in Bacterial Infection

Cited by 7 publications

References 24 publications

Green synthesis of silver nanoparticles mediated Azadirachta indica extract and study of their characterization, molecular docking, and antibacterial activity

Green synthesis of silver nanoparticles mediated Azadirachta indica extract and study of their characterization, molecular docking, and antibacterial activity

Design for the Colon Cancer Inhibitors Targeting Thymidylate Kinase by Using Insilico Studies

Molecular Docking Dynamics of Selected Benzylidene Amino Phenyl Acetamides as TMK Inhibitors Using High Throughput Virtual Screening (Htvs)

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