Investigating the anti-streptococcal biofilm effect of ssDNA aptamer-silver nanoparticles complex on a titanium-based substrate

Hosseini, Barumand; Behbahani, Mandana; Dini, Ghasem; Mohabatkar, Hassan; Keyhanfar, Mehrnaz

doi:10.1039/d2ra04112j

Cited by 8 publications

(5 citation statements)

References 87 publications

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“…Then, they performed molecular dynamics to choose the strongest and the highest stable complex of the aptamer-SARS-CoV-2 main protease. Hosseini et al [ 51 ] designed an ssDNA aptamer via bioinformatics tools and then employed that aptamer in conjugation with silver nanoparticles for inhibition of biofilm formation on the surface of titanium implants. In their study, UNAFold and H-DOCK online servers were used for secondary structure prediction and molecular docking analysis, respectively.…”

Section: Resultsmentioning

confidence: 99%

A label-free G-quadruplex aptamer/gold nanoparticle-based colorimetric biosensor for rapid detection of bovine viral diarrhea virus genotype 1

Rabiei,

Mohabatkar,

Behbahani

2024

PLoS ONE

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Bovine viral diarrhea virus (BVDV) is the cause of bovine viral diarrhea disease, one of the most economically important livestock diseases worldwide. The majority of BVD disease control programs rely on the detection and then elimination of persistent infection (PI) cattle, as the continuing source of disease. The main purpose of this study was to design and develop an accurate G-quadruplex-based aptasensor for rapid and simple detection of BVDV-1. In this work, we utilized in silico techniques to design a G-quadruplex aptamer specific for the detection of BVDV-1. Also, the rationally designed aptamer was validated experimentally and was used for developing a colorimetric biosensor based on an aptamer-gold nanoparticle system. Firstly, a pool of G-quadruplex forming ssDNA sequences was constructed. Then, based on the stability score in secondary and tertiary structures and molecular docking score, an aptamer (Apt31) was selected. In the experimental part, gold nanoparticles (AuNPs) with an average particle size of 31.7 nm were synthesized and electrostatically linked with the Apt31. The colorimetric test showed that salt-induced color change of AuNPs from red to purple-blue occurs only in the presence of BVDV-Apt31 complex, after 20 min. These results approved the specificity of Apt31 for BVDV. Furthermore, our biosensor could detect the virus at as low as 0.27 copies/ml, which is an acceptable value in comparison to the qPCR method. The specificity of the aptasensor was confirmed through cross-reactivity testing, while its selectivity was confirmed through plasma testing. The sample analysis showed 90% precision and 94% accuracy. It was concluded that the biosensor was adequately sensitive and specific for the detection of BVDV in plasma samples and could be used as a simple and rapid method on the farm.

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Section: Resultsmentioning

confidence: 99%

A label-free G-quadruplex aptamer/gold nanoparticle-based colorimetric biosensor for rapid detection of bovine viral diarrhea virus genotype 1

Rabiei,

Mohabatkar,

Behbahani

2024

PLoS ONE

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“…The remaining selected models were taken for further docking studies. The modeled structures of fibronectin/fibrinogen binding protein (FBP) from S. mutans , phospholipase D (F13) protein of monkeypox virus, 3-chymotrypsin and papain-like proteases of SARS-CoV2, and U box domain-containing protein gene (GsPUB8) from Glycine soja were all validated using the Ramachandran plot [ 38 , 39 , 40 , 41 ].…”

Section: Discussionmentioning

confidence: 99%

Pharmacoinformatics-Based Approach for Uncovering the Quorum-Quenching Activity of Phytocompounds against the Oral Pathogen, Streptococcus mutans

Marimuthu,

Murugesan,

Babkiewicz

et al. 2023

Molecules

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Streptococcus mutans, a gram-positive oral pathogen, is the primary causative agent of dental caries. Biofilm formation, a critical characteristic of S. mutans, is regulated by quorum sensing (QS). This study aimed to utilize pharmacoinformatics techniques to screen and identify effective phytochemicals that can target specific proteins involved in the quorum sensing pathway of S. mutans. A computational approach involving homology modeling, model validation, molecular docking, and molecular dynamics (MD) simulation was employed. The 3D structures of the quorum sensing target proteins, namely SecA, SMU1784c, OppC, YidC2, CiaR, SpaR, and LepC, were modeled using SWISS-MODEL and validated using a Ramachandran plot. Metabolites from Azadirachta indica (Neem), Morinda citrifolia (Noni), and Salvadora persica (Miswak) were docked against these proteins using AutoDockTools. MD simulations were conducted to assess stable interactions between the highest-scoring ligands and the target proteins. Additionally, the ADMET properties of the ligands were evaluated using SwissADME and pkCSM tools. The results demonstrated that campesterol, meliantrol, stigmasterol, isofucosterol, and ursolic acid exhibited the strongest binding affinity for CiaR, LepC, OppC, SpaR, and Yidc2, respectively. Furthermore, citrostadienol showed the highest binding affinity for both SMU1784c and SecA. Notably, specific amino acid residues, including ASP86, ARG182, ILE179, GLU143, ASP237, PRO101, and VAL84 from CiaR, LepC, OppC, SecA, SMU1784c, SpaR, and YidC2, respectively, exhibited significant interactions with their respective ligands. While the docking study indicated favorable binding energies, the MD simulations and ADMET studies underscored the substantial binding affinity and stability of the ligands with the target proteins. However, further in vitro studies are necessary to validate the efficacy of these top hits against S. mutans.

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“…Then, the samples were stained with crystal violet and the OD value was measured by a microplate reader at 590 nm. For biofilm inhibition, Cy‐HMPBs/CH (15 μg/mL) was co‐cultured with the bacteria and irradiated with or without the NIR laser 43,44 . The absorbance was measured using the same method.…”

Section: Methodsmentioning

confidence: 99%

“…For biofilm inhibition, Cy-HMPBs/CH (15 μg/mL) was co-cultured with the bacteria and irradiated with or without the NIR laser. 43,44 The absorbance was measured using the same method.…”

Section: Antibacterial Capability Evaluationmentioning

confidence: 99%

Cypate‐loaded hollow mesoporous Prussian blue nanoparticle/hydrogel system for efficient photodynamic therapy/photothermal therapy dual‐modal antibacterial therapy

Xing,

Dong,

Zhang

et al. 2023

J Biomedical Materials Res

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Infectious diseases caused by pathogenic microorganisms are a significant burden on public health and the economic stability of societies all over the world. The appearance of drug‐resistant bacteria has severely blocked the effectiveness of conventional antibiotics. Therefore, developing novel antibiotic‐free strategies to combat bacteria holds huge potential for maximizing validity and minimizing the risk of enhancing bacterial resistance. Herein, a cypate‐loaded hollow mesoporous Prussian blue nanoparticles (Cy‐HMPBs) was built to achieve the PDT/PTT synergistic antimicrobial therapy. The carbomer hydrogel (CH) was combined with the Cy‐HMPBs to form a nanoparticle/hydrogel therapeutic system (Cy‐HMPBs/CH) to reach the goal of local delivery of antimicrobial cargo. The low concentration of Cy‐HMPBs/CH receives over 99% of antimicrobial ability against Escherichia coli and Staphylococcus aureus upon near‐infrared (NIR) irradiation. More importantly, Cy‐HMPBs/CH has favorable biocompatibility and can play therapeutic effects only after laser irradiation, indicating the on‐demand therapy at the targeted region to avert side effects on healthy tissue. This study provides ideas for the design of an antibiotic‐free antimicrobial strategy against infectious diseases.

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Investigating the anti-streptococcal biofilm effect of ssDNA aptamer-silver nanoparticles complex on a titanium-based substrate

Abstract: Silver nanoparticles attached to the specific aptamer forStreptococcus mutans, can significantly remove the biofilm of this bacterium attached to the surface of the titanium implant.

Cited by 8 publications

References 87 publications

A label-free G-quadruplex aptamer/gold nanoparticle-based colorimetric biosensor for rapid detection of bovine viral diarrhea virus genotype 1

A label-free G-quadruplex aptamer/gold nanoparticle-based colorimetric biosensor for rapid detection of bovine viral diarrhea virus genotype 1

Pharmacoinformatics-Based Approach for Uncovering the Quorum-Quenching Activity of Phytocompounds against the Oral Pathogen, Streptococcus mutans

Cypate‐loaded hollow mesoporous Prussian blue nanoparticle/hydrogel system for efficient photodynamic therapy/photothermal therapy dual‐modal antibacterial therapy

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