De novo post-SELEX optimization of a G-quadruplex DNA aptamer binding to marine toxin gonyautoxin 1/4

Song, Menghua; Gan, Li; Zhang, Qi; Liu, Jianping; Huang, Qiang

doi:10.1016/j.csbj.2020.10.041

Cited by 26 publications

(22 citation statements)

References 48 publications

(36 reference statements)

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“…Any drug molecule that effectively inhibits the proteolysis function of TMPRSS2 has to be bound to the catalytic amino-acids and/or the substrate-binding regions. To capture the dynamic association process of a given drug with the protein receptor, atomic-level, unbiased MD simulation is an effective tool [40] , [41] , [50] . To simulate those association processes for Camostat and Nafamostat in an aqueous environment, we used the mentioned TMPRSS2-ECD structure at 200 ns to establish the simulation systems.…”

Section: Resultsmentioning

confidence: 69%

“…3 . As supported by our previous studies [40] , [41] , this calculation method of binding free-energy is fast and reliable for analyzing large numbers of inhibitor-receptor snapshot complexes in the MD simulations. The calculations for the trajectories in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…As in our previous studies [40] , [41] , we used AutoDockTools [42] to calculate the free energy of a drug (Camostat or Nafamostat) that bind to TMPRSS2-ECD in the simulation snapshots. AutoDockTools uses the AutoDock 4.1 semi-empirical free energy force field to estimate the free energy of a small-molecular drug binding to a protein receptor based on their drug-protein complex, With the given complex, the binding free energy (

) equals to the change in the free energy of the drug from the unbound state to the bound state:

where the first two terms are the energies of the drug-protein complex in the bound state, consisting of the intermolecular and intramolecular free energies.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Spontaneous binding of potential COVID-19 drugs (Camostat and Nafamostat) to human serine protease TMPRSS2

Zhu

Song

et al. 2021

Computational and Structural Biotechnology Journal

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Section: Resultsmentioning

confidence: 69%

Section: Resultsmentioning

confidence: 99%

) equals to the change in the free energy of the drug from the unbound state to the bound state:

where the first two terms are the energies of the drug-protein complex in the bound state, consisting of the intermolecular and intramolecular free energies.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Spontaneous binding of potential COVID-19 drugs (Camostat and Nafamostat) to human serine protease TMPRSS2

Zhu

Song

et al. 2021

Computational and Structural Biotechnology Journal

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“…The aptamer of HLA-G5 was screened from a DNA library using methods from the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) (19)(20)(21)(22). Briefly, the carboxyl magnetic beads were incubated with HLA-G5 protein (concentration of 0.35 mg/mL) for 40 min on a shaker at room temperature.…”

Section: Selex Methods To Prepare the Aptamer Of Hla-g5mentioning

confidence: 99%

Novel nucleic acid aptamer gold (Au)-nanoparticles (AuNPs-AptHLA-G5-1 and AuNPs-AptHLA-G5-2) to detect the soluble human leukocyte antigen G5 subtype (HLA-G5) in liquid samples

Wang

Yao

2021

Ann Transl Med

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Background: The human leukocyte antigen G5 subtype (HLA-G5) is a major histocompatibility complex (MHC) molecule that is selectively expressed at the maternal-foetal tissue interface and is required for the successful implantation of the in vitro fertilized embryo. It is critical to detect HLA-G5, especially HLA-G5 expression in embryo fluid, during in vitro embryo incubation and culture. However, the specificity and sensitivity of traditional ELISA methods to detect sHLA-G5 are insufficient. This work aimed to explore novel nucleic acid aptamer gold (Au)-nanoparticles to detect soluble HLA-G5 in liquid samples.Methods: Soluble HLA-G5 was obtained using a prokaryotic expression system, and two novel aptamers (HLA-G5-Apt1 and HLA-G5-Apt2) detecting HLA-G5 were screened by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. Small (10 nm) gold nanoparticles (AuNPs) were incubated with AptHLAs to form two novel nucleic acid aptamers: Au-nanoparticles (AuNPs-AptHLA-G5-1 and AuNPs-AptHLA-G5-2). Results:The results showed that AptHLA-G5-1 and AptHLA-G5-2 have a high affinity for HLA-G5 and can detect its presence in liquid samples. Using the colorimetric sensing method, AuNPs-AptHLA-G1 had a detection limit as low as 20 ng/mL (recovery range between 98.7% to 102.0%), while AuNPs-AptHLA-G2 had a detection limit as low as 20 ng/mL (recovery range between 98.9% to 103.6%).Conclusions: Our work demonstrates that novel AuNPs are efficient detectors for HLA-G5 and are useful for diagnosis and treatment in the field of obstetrics-gynaecology.

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“…Aptamers have various advantages over protein-based drugs, such as antibodies or peptides [ 16 ]. Aptamers are short and single-stranded oligonucleotides and have been reported to be antagonists against various target proteins through phylogenetic and exponential enrichment (SELEX) analysis [ 17 ]. Aptamers are chemical antibodies with three-dimensional structures; therefore, they have excellent thermal stability and high affinity and specificity for the homologous protein targets and display good biocompatibility [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

An Aptamer-Based Antagonist against the Receptor for Advanced Glycation End-Products (RAGE) Blocks Development of Colorectal Cancer

Zheng

Zhu

et al. 2021

Mediators of Inflammation

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Tumor angiogenesis plays a crucial role in colorectal cancer development. Dysregulation of the receptor for the advanced glycation end-products (RAGE) transmembrane signaling mediates inflammation, resulting in various cancers. However, the mechanism of the RAGE signaling pathway in modulating development of colorectal cancer has not been explored. In this study, an aptamer-based RAGE antagonist (Apt-RAGE) was used to inhibit interaction between RAGE and S100B, thus blocking downstream NFκB-mediated signal transduction. In vitro results showed that Apt-RAGE effectively inhibited S100B-dependent and S100B-independent RAGE/NFκB activation in colorectal HCT116 cancer cells, thus decreasing proliferation and migration of cells. Notably, expression and secretion of VEGF-A were inhibited, implying that Apt-RAGE can be used as an antiangiogenesis agent in tumor therapy. Moreover, Apt-RAGE inhibited tumor growth and microvasculature formation in colorectal tumor-bearing mice. Inhibition of angiogenesis by Apt-RAGE was positively correlated with suppression of the RAGE/NFκB/VEGF-A signaling. The findings of this study show that Apt-RAGE antagonist is a potential therapeutic agent for treatment of colorectal cancer.

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De novo post-SELEX optimization of a G-quadruplex DNA aptamer binding to marine toxin gonyautoxin 1/4

Abstract: Graphical abstract

Cited by 26 publications

References 48 publications

Spontaneous binding of potential COVID-19 drugs (Camostat and Nafamostat) to human serine protease TMPRSS2

Spontaneous binding of potential COVID-19 drugs (Camostat and Nafamostat) to human serine protease TMPRSS2

Novel nucleic acid aptamer gold (Au)-nanoparticles (AuNPs-AptHLA-G5-1 and AuNPs-AptHLA-G5-2) to detect the soluble human leukocyte antigen G5 subtype (HLA-G5) in liquid samples

An Aptamer-Based Antagonist against the Receptor for Advanced Glycation End-Products (RAGE) Blocks Development of Colorectal Cancer

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