Production, characterization and antibacterial activity of silver nanoparticles produced by Fusarium oxysporum and monitoring of protein-ligand interaction through in-silico approaches

2019 ◽  
Vol 129 ◽  
pp. 136-145 ◽  
Author(s):  
Shilpi Srivastava ◽  
Atul Bhargava ◽  
Neelam Pathak ◽  
Prachi Srivastava
Keyword(s):  
Silver Nanoparticles ◽  
Antibacterial Activity ◽  
Fusarium Oxysporum ◽  
In Silico ◽  
Ligand Interaction ◽  
Protein Ligand Interaction

scholarly journals In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

2021 ◽  
Author(s):  
Nícia Rosário-Ferreira ◽  
Salete J. Baptista ◽  
Carlos A. V. Barreto ◽  
Filipe E. P. Rodrigues ◽  
Tomás F. D. Silva ◽  
...  
Keyword(s):  
In Silico ◽  
Ligand Interaction ◽  
Protein Ligand Interaction ◽  
End To End

In-silico analysis of angiotensin converting enzyme 2 (ACE2) of livestock, pet and poultry animals to determine its susceptibility to SARS–CoV- 2 infection

2020 ◽  
Vol 23 ◽  
Author(s):  
Aman Kumar ◽  
Anil Panwar ◽  
Kanisht Batra ◽  
Sachinandan Dey ◽  
Sushila Maan
Keyword(s):  
In Silico ◽  
Binding Capacity ◽  
In Silico Analysis ◽  
Ligand Interaction ◽  
Angiotensin Converting Enzyme 2 ◽  
Animal Management ◽  
In Silico Study ◽  
Protein Ligand Interaction ◽  
Novel Coronavirus ◽  
Almost All

Background: Novel coronavirus SARS-CoV-2 is responsible of COVID-19 pandemic. It was first reported in Wuhan, China in December, 2019 and despite the tremendous efforts to control the disease, it has now spread almost all over the world.The interaction of SARS-CoV-2spike protein and its acceptor protein ACE2 is an important issue in determining viralhost range and cross-species infection, while the binding capacity of spike protein toACE2 of different species is unknown. Objective: The present study has been conducted to determine the susceptibility of livestock, poultry and pets to SARSCoV-2. Methods: We evaluated the receptor-utilizing capability of ACE2sfrom various species by sequence alignment,phylogenetic clustering and protein-ligand interaction studies with the currently knownACE2s utilized by SARS-CoV-2. Result: In-silico study predicted that SARS-CoV-2 tends to utilize ACE2s ofvarious animal species with varied possible interactions and theprobability ofthe receptor utilization will be greater in horse and poor in chicken followed by ruminants. Conclusion: Present studypredicted that SARS-CoV-2 tends to utilize ACE2s ofvarious livestock and poultry species with greater probability in equine and poor in chicken. Study may provide important insights into the animal models for SARSCoV-2 and animal management for COVID-19 control.

Synthesis, In-Vitro and In-Silico Evaluation of Silver Nanoparticles with Root Extract of Withania somnifera for Antibacterial Activity via Binding of Penicillin-Binding Protein-4

2020 ◽  
Vol 21 (15) ◽  
pp. 1674-1687
Author(s):  
Isha Gaurav ◽  
Tanuja Singh ◽  
Abhimanyu Thakur ◽  
Gaurav Kumar ◽  
Parth Rathee ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Mechanism Of Action ◽  
In Silico ◽  
Withania Somnifera ◽  
Withaferin A ◽  
Root Extract ◽  
Penicillin Binding Protein ◽  
Withanolide A

Background: Metal Nanoparticles (NPs) have been widely used for various applications in biomedical sciences, including in drug delivery, and as therapeutic agents, but limited owing to their toxicity towards the healthy tissue. This warrants an alternative method, which can achieve the desired activity with much reduced or no toxicity. Being a biological product, Withania somnifera (W. somnifera) is environment friendly, besides being less toxic as compared to metal-based NPs. However, the exact mechanism of action of W. somnifera for its antibacterial activities has not been studied so far. Objective: To develop “silver nanoparticles with root extract of W. somnifera (AgNPs-REWS)” for antimicrobial and anticancer activities. Furthermore, the analysis of their mechanism of action will be studied. Methods: Using the in-silico approach, the molecular docking study was performed to evaluate the possible antibacterial mechanism of W. somnifera phytochemicals such as Anaferine, Somniferine, Stigmasterol, Withaferin A, Withanolide- A, G, M, and Withanone by the inhibition of Penicillin- Binding Protein 4 (PBP4). Next, we utilized a bottom-up approach for the green synthesis of AgNPs- REWS, performed an in-detail phytochemical analysis, confirmed the AgNPs-REWS by SEM, UVvisible spectroscopy, XRD, FT-IR, and HPLC. Eventually, we examined their antibacterial activity. Results: The result of molecular docking suggests that WS phytochemicals (Somniferine, Withaferin A, Withanolide A, Withanolide G, Withanolide M, and Withanone) possess the higher binding affinity toward the active site of PBP4 as compared to the Ampicillin (-6.39 kcal/mol) reference molecule. These phytochemicals predicted as potent inhibitors of PBP4. Next, as a proof-of-concept, AgNPs- REWS showed significant antibacterial effect as compared to crude, and control; against Xanthomonas and Ralstonia species. Conclusion: The in-silico and molecular docking analysis showed that active constituents of W. somnifera such as Somniferine, Withaferin A, Withanolide A, Withanolide G, Withanolide M, and Withanone possess inhibition potential for PBP4 and are responsible for the anti-bacterial property of W. somnifera extract. This study also establishes that AgNPs via the green synthesis with REWS showed enhanced antibacterial activity towards pathogenic bacteria.

Identification of potential histone deacetylase inhibitory biflavonoids from Garcinia kola (Guttiferae) using in silico protein-ligand interaction

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Kayode E. Adewole ◽  
Ahmed A. Ishola ◽  
Blessing O. Omolaso
Keyword(s):  
In Silico ◽  
Histone Deacetylases ◽  
Hdac Inhibitors ◽  
Intimate Relationship ◽  
Binding Affinities ◽  
Ligand Interaction ◽  
Garcinia Kola ◽  
Discovery Studio ◽  
Limited Success ◽  
Protein Ligand Interaction

Abstract Overactivity of histone deacetylases (HDACs) is the underlying cause of some cancers, thus, inhibiting their overactivities is a rational treatment option. However, endeavors to employ current anti-HDACs agents in cancer treatment have yielded limited success. Consequently, there is need to explore anti-HDACs natural products, especially from plants sources, because of the intimate relationship plant products and drug discovery have enjoyed over the centuries. To identify possible HDACs inhibitors, Garcinia kola (Guttiferae) seed-derived compounds were screened in silico for HDAC-inhibitory tendencies because of their reported anticancer potentials. Fifteen G. kola-derived compounds and givinostat were docked with five selected HDACs using AutodockVina, while the binding interactions of the compounds with high binding affinities for the five HDACs were viewed with Discovery Studio Visualizer BIOVIA, 2016. Results indicated that four of the compounds studied, including amentoflavone, Garcinia biflavonoid 1, Garcinia biflavonoid 2 and kolaflavanone have higher binding propensity for all the five HDACs relative to givinostat, the standard HDAC inhibitor. This study indicated that inhibition of HDAC might be another key mechanism accountable for the bioactivities of G. kola and its intrinsic compounds. The results from this study implied that the compounds could be further investigated as drugable HDAC inhibitors with potential pharmacological applications in the treatment of cancers.

Antibacterial Activity of Biodegradable Particles based on Chitosan Containing Colloidal Silver

2020 ◽  
Vol 36 (4) ◽  
pp. 87-93
Author(s):  
V.Yu. Reshetova ◽  
A.F. Krivoshchepov ◽  
I.A. Butorova ◽  
N.B. Feldman ◽  
S.V. Lutsenko ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Antibacterial Activity ◽  
Polymer Matrix ◽  
Adipic Acid ◽  
Antibacterial Effect ◽  
Academic Excellence ◽  
Colloidal Silver ◽  
Scanning Electron Microscopy Data ◽  
Covalent Bonds ◽  
Agar Diffusion Test

Chitosan beads with colloidal silver nanoparticles inclued in the polymer matrix have been obtained by the introduction of chitosan into an acidified nanosilver sol. Dual interconnection of drops of the resulting solution was then carried out by ionotropic gelation at the first stage and covalent crosslinking of the polymer matrix with adipic acid at the second stage. The surface morphology of the obtained beads was studied by scanning electron microscopy. Data of Fourier transform IR spectroscopy confirmed the formation of covalent bonds between chitosan and adipic acid. The antibacterial activity of obtained beads against S. aureus and E. coli was evaluated using agar diffusion test. It was shown that the сhitosan beads modified with nanostructured silver exhibited an antibacterial effect against the tested strains, and they can be used as a basis for creating biodegradable wound healing dressings with a prolonged antibacterial effect. chitosan, silver nanoparticles, antibacterial activity, wound dressings This work was supported by the "Russian Academic Excellence Project 5-100". The study was carried out with the financial support of the Russian Foundation for Basic Research in the framework of the Scientific Project no. 18-29-18039.

Green Synthesis of Silver Nanoparticles Using Artocarpus hirsutus Seed Extract and its Antibacterial Activity

2020 ◽  
Vol 21 (10) ◽  
pp. 980-989
Author(s):  
Sampath Shobana ◽  
Sunderam Veena ◽  
S.S.M. Sameer ◽  
K. Swarnalakshmi ◽  
L.A. Vishal
Keyword(s):  
Silver Nanoparticles ◽  
Cell Wall ◽  
Antibacterial Activity ◽  
Listeria Monocytogenes ◽  
Nanoparticle Synthesis ◽  
Enterobacter Aerogenes ◽  
Seed Extract ◽  
Diffusion Method ◽  
Multi Drug Resistance ◽  
Gastrointestinal Bacteria

Aims: To evaluate the antibacterial activity of Artocarpus hirsutus mediated seed extract for nanoparticle synthesis. Background: Gastrointestinal bacteria are known for causing deadly infections in humans. They also possess multi-drug resistance and interfere with clinical treatments. Applied nanotechnology has been known to combat such infectious agents with little interference from their special attributes. Here we synthesize silver nanoparticles from Artocarpus hirsutus seed extract against two gastro-intestinal bacterial species: Enterobacter aerogenes and Listeria monocytogenes. Objective: To collect, dry, and process seeds of Artocarpus hirsutus for nanoparticle synthesis. To evaluate the morphological interaction of silver nanoparticles with bacteria. Methods: Artocarpus hirsutus seeds were collected and processed and further silver nanoparticles were synthesized by the co-precipitation method. The synthesized nanoparticles were characterized using XRD, UV, FTIR, and SEM. These nanoparticles were employed to study the antibacterial activity of nanoparticles against Enterobacter aerogenes and Listeria monocytogenes using well diffusion method. Further, morphological interaction of silver nanoparticles on bacteria was studied using SEM. Result: Silver nanoparticles were synthesized using Artocarpus hirsutus seed extract and characterization studies confirmed that silver nanoparticles were spherical in shape with 25-40 nm size. Antibacterial study exhibited better activity against Enterobacter aerogenes with a maximum zone of inhibition than on Listeria monocytogenes. SEM micrographs indicated that Enterobacter aerogenes bacteria were more susceptible to silver nanoparticles due to the absence of cell wall. Also, the size and charge of silver nanoparticles enable easy penetration of the bacterial cell wall. Conclusion: In this study, silver nanoparticles were synthesized using the seed extract of Artocarpus hirsutus for the first time exploiting the fact that Moraceae species have high phytonutrient content which aided in nanoparticle synthesis. This nanoparticle can be employed for large scale synthesis which when coupled with the pharmaceutical industry can be used to overcome the problems associated with conventional antibiotics to treat gastrointestinal bacteria.

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