Surface plasmon resonance aptasensing and computational analysis of Staphylococcus aureus IsdA surface protein.

Staphylococcus aureus (S. aureus), a common foodborne pathogen, poses significant public health challenges due to its association with various infectious diseases. A key player in its pathogenicity, which is the IsdA protein, is an essential virulence factor in S. aureus infections. In this work, we present an integrated in-silico and experimental approach using MD simulations and surface plasmon resonance (SPR)-based aptasensing measurements to investigate S. aureus biorecognition via IsdA surface protein binding. SPR, a powerful real-time and label-free technique, was utilized to characterize interaction dynamics between the aptamer and IsdA protein, and MD simulations was used to characterize the stable and dynamic binding regions. By characterizing and optimizing pivotal parameters such as aptamer concentration and buffer conditions, we determined the aptamer's binding performance. Under optimal conditions of pH 7.4 and 150 mM NaCl concentration, the kinetic parameters were determined; ka = 3.789 × 104/Ms, kd = 1.798 × 103/s, and KD = 4.745 × 10-8 M. The simulations revealed regions of interest in the IsdA-aptamer complex. Region I, which includes interactions between amino acid residues H106 and R107 and nucleotide residues 9G, 10U, 11G and 12U of the aptamer, had the strongest interaction, based on ΔG and B-factor values, and hence contributed the most to the stability of the interaction. Region II, which covers residue 37A reflects the dynamic nature of the interaction due to frequent contacts. The approach presents a rigorous characterization of aptamer-IsdA binding behavior, supporting the potential application of the IsdA-binding aptamer system for S. aureus biosensing.

Computational generation and characterization of IsdA-binding aptamers with single-molecule FRET analysis.

Staphylococcus aureus is a major foodborne bacterial pathogen. Early detection of S. aureus is crucial to prevent infections and ensure food quality. The iron-regulated surface determinant protein A (IsdA) of S. aureus is a unique surface protein necessary for sourcing vital iron from host cells for the survival and colonization of the bacteria. The function, structure, and location of the IsdA protein make it an important protein for biosensing applications relating to the pathogen. Here, we report an in-silico approach to develop and validate high-affinity binding aptamers for the IsdA protein detection using custom-designed in-silico tools and single-molecule Fluorescence Resonance Energy Transfer (smFRET) measurements. We utilized in-silico oligonucleotide screening methods and metadynamics-based methods to generate 10 aptamer candidates and characterized them based on the Dissociation Free Energy (DFE) of the IsdA-aptamer complexes. Three of the aptamer candidates were shortlisted for smFRET experimental analysis of binding properties. Limits of detection in the low picomolar range were observed for the aptamers, and the results correlated well with the DFE calculations, indicating the potential of the in-silico approach to support aptamer discovery. This study showcases a computational SELEX method in combination with single-molecule binding studies deciphering effective aptamers against S. aureus IsdA, protein. The established approach demonstrates the ability to expedite aptamer discovery that has the potential to cut costs and predict binding efficacy. The application can be extended to designing aptamers for various protein targets, enhancing molecular recognition, and facilitating the development of high-affinity aptamers for multiple uses.

Selective adsorption of organic dyes from aqueous environment using fermented maize extract-enhanced graphene oxide-durian shell derived activated carbon composite.

A secure aquatic environment is essential for both aquatic and terrestrial life. However, rising populations and the industrial revolution have had a significant impact on the quality of the water environment. Despite the implementation of strong and adapted environmental policies for water treatment worldwide, the issue of organic dyes in wastewater remains challenging. Thus, this study aimed to develop an efficient, cost-effective, and sustainable material to treat methylene blue (MB) in an aqueous environment. In this research, maize extract solution (MES) was utilized as a green cross-linker to induce precipitation, conjugation, and enhance the adsorption performance of graphene oxide (GO) cross-linked with durian shell activated carbon (DSAC), resulting in the formation of a GO@DSAC composite. The composite was investigated for its adsorptive performance toward MB in aqueous media. The physicochemical characterization demonstrated that the cross-linking method significantly influenced the porous structure and surface chemistry of GO@DSAC. BET analysis revealed that the GO@DSAC exhibited dominant mesopores with a surface area of 803.67 m2/g. EDX and XPS measurements confirmed the successful cross-linking of GO with DSAC. The adsorption experiments were well described by the Harkin-Jura model and they followed pseudo-second order kinetics. The maximum adsorption capacity reached 666.67 mg/g at 318 K. Thermodynamic evaluation indicated a spontaneous, feasible, and endothermic in nature. Regenerability and reusability investigations demonstrated that the GO@DSAC composite could be reused for up to 10 desorption-adsorption cycles with a removal efficiency of 81.78%. The selective adsorptive performance of GO@DSAC was examined in a binary system containing Rhodamine B (RhB) and methylene orange (MO). The results showed a separation efficiency (α) of 98.89% for MB/MO and 93.66% for MB/RhB mixtures, underscoring outstanding separation capabilities of the GO@DSAC composite. Overall, the GO@DSAC composite displayed promising potential for the effective removal of cationic dyes from wastewater.

Magnetic Nanoparticles for Protein Separation and Purification.

Proteins are essential for various functions such as brain activity and muscle contraction in humans. Even though food is a source of proteins, the bioavailability of proteins in most foods is usually limited due to matrix interaction with other biomolecules. Thus, it is essential to extract these proteins and provide them as a nutraceutical supplement to maintain protein levels and avoid protein deficiency. Hence, protein purification and extraction from natural sources are highly significant in biomedical applications. Chromatography, crude mechanical disruption, use of extractive chemicals, and electrophoresis are some of the methods applied to isolate specific proteins. Even though these methods possess several advantages, they are unable to extract specific proteins with high purity. A suitable alternative is the use of nanoparticles, which can be beneficial in protein purification and extraction. Notably, magnetic iron and iron-based nanoparticles have been employed in protein extraction processes and can be reused via demagnetization due to their magnetic property, smaller size, morphology, high surface-to-volume ratio, and surface charge-mediated property. This chapter is a summary of various magnetic nanoparticles (MNPs) that can be used for the biomolecular separation of proteins.

FRET-Based Single-Molecule Detection of Pathogen Protein IsdA Using Computationally Selected Aptamers.

Iron-regulated surface determinant protein A (IsdA) is a key surface protein found in the foodborne bacteria─Staphylococcus aureus (S. aureus)─which is known to be critical for bacterial survival and colonization. S. aureus is pathogenic and has been linked to foodborne diseases; thus, early detection is critical to prevent diseases caused by this bacterium. Despite IsdA being a specific marker for S. aureus and several detection methods have been developed for sensitive detection of this bacteria such as cell culture, nucleic acids amplification, and other colorimetric and electrochemical methods, the detection of S. aureus through IsdA is underdeveloped. Here, by combining computational generation of target-guided aptamers and fluorescence resonance energy transfer (FRET)-based single-molecule analysis, we presented a widely applicable and robust detection method for IsdA. Three different RNA aptamers specific to the IsdA protein were identified and their ability to switch a FRET construct to a high-FRET state in the presence of protein was verified. The presented approach demonstrated the detection of IsdA down to picomolar levels (×10-12 M, equivalent to ∼1.1 femtomoles IsdA) with a dynamic range extending to ∼40 nM. The FRET-based single-molecule technique that we reported here is capable of detecting the foodborne pathogen protein IsdA with high sensitivity and specificity and has a broader application in the food industry and aptamer-based sensing field by enabling quantitative detection of a wide range of pathogen proteins.

Novel Concepts for Graphene-Based Nanomaterials Synthesis for Phenol Removal from Palm Oil Mill Effluent (POME).

In recent years, the global population has increased significantly, resulting in elevated levels of pollution in waterways. Organic pollutants are a major source of water pollution in various parts of the world, with phenolic compounds being the most common hazardous pollutant. These compounds are released from industrial effluents, such as palm oil milling effluent (POME), and cause several environmental issues. Adsorption is known to be an efficient method for mitigating water contaminants, with the ability to eliminate phenolic contaminants even at low concentrations. Carbon-based materials have been reported to be effective composite adsorbents for phenol removal due to their excellent surface features and impressive sorption capability. However, the development of novel sorbents with higher specific sorption capabilities and faster contaminant removal rates is necessary. Graphene possesses exceptionally attractive chemical, thermal, mechanical, and optical properties, including higher chemical stability, thermal conductivity, current density, optical transmittance, and surface area. The unique features of graphene and its derivatives have gained significant attention in the application of sorbents for water decontamination. Recently, the emergence of graphene-based adsorbents with large surface areas and active surfaces has been proposed as a potential alternative to conventional sorbents. The aim of this article is to discuss novel synthesis approaches for producing graphene-based nanomaterials for the adsorptive uptake of organic pollutants from water, with a special focus on phenols associated with POME. Furthermore, this article explores adsorptive properties, experimental parameters for nanomaterial synthesis, isotherms and kinetic models, mechanisms of nanomaterial formation, and the ability of graphene-based materials as adsorbents of specific contaminants.

Bioaffinity Nanoprobes for Foodborne Pathogen Sensing.

Bioaffinity nanoprobes are a type of biosensor that utilize the specific binding properties of biological molecules, such as antibodies, enzymes, and nucleic acids, for the detection of foodborne pathogens. These probes serve as nanosensors and can provide highly specific and sensitive detection of pathogens in food samples, making them an attractive option for food safety testing. The advantages of bioaffinity nanoprobes include their ability to detect low levels of pathogens, rapid analysis time, and cost-effectiveness. However, limitations include the need for specialized equipment and the potential for cross-reactivity with other biological molecules. Current research efforts focus on optimizing the performance of bioaffinity probes and expanding their application in the food industry. This article discusses relevant analytical methods, such as surface plasmon resonance (SPR) analysis, Fluorescence Resonance Energy Transfer (FRET) measurements, circular dichroism, and flow cytometry, that are used to evaluate the efficacy of bioaffinity nanoprobes. Additionally, it discusses advances in the development and application of biosensors in monitoring foodborne pathogens.

Target-Specific Delivery and Bioavailability of Pharmaceuticals via Janus and Dendrimer Particles.

Nanosized Janus and dendrimer particles have emerged as promising nanocarriers for the target-specific delivery and improved bioavailability of pharmaceuticals. Janus particles, with two distinct regions exhibiting different physical and chemical properties, provide a unique platform for the simultaneous delivery of multiple drugs or tissue-specific targeting. Conversely, dendrimers are branched, nanoscale polymers with well-defined surface functionalities that can be designed for improved drug targeting and release. Both Janus particles and dendrimers have demonstrated their potential to improve the solubility and stability of poorly water-soluble drugs, increase the intracellular uptake of drugs, and reduce their toxicity by controlling the release rate. The surface functionalities of these nanocarriers can be tailored to specific targets, such as overexpressed receptors on cancer cells, leading to enhanced drug efficacy The design of these nanocarriers can be optimized by tuning the size, shape, and surface functionalities, among other parameters. The incorporation of Janus and dendrimer particles into composite materials to create hybrid systems for enhancing drug delivery, leveraging the unique properties and functionalities of both materials, can offer promising outcomes. Nanosized Janus and dendrimer particles hold great promise for the delivery and improved bioavailability of pharmaceuticals. Further research is required to optimize these nanocarriers and bring them to the clinical setting to treat various diseases. This article discusses various nanosized Janus and dendrimer particles for target-specific delivery and bioavailability of pharmaceuticals. In addition, the development of Janus-dendrimer hybrid nanoparticles to address some limitations of standalone nanosized Janus and dendrimer particles is discussed.

Editorial to the IJMS Special Issue "Aptamer-Mediated Cancer Theranostics".

Aptamers have emerged as a new generation of bioaffinity probes with enhanced target binding specificity and selectivity [...].

Development of Janus Particles as Potential Drug Delivery Systems for Diabetes Treatment and Antimicrobial Applications.

Janus particles have emerged as a novel and smart material that could improve pharmaceutical formulation, drug delivery, and theranostics. Janus particles have two distinct compartments that differ in functionality, physicochemical properties, and morphological characteristics, among other conventional particles. Recently, Janus particles have attracted considerable attention as effective particulate drug delivery systems as they can accommodate two opposing pharmaceutical agents that can be engineered at the molecular level to achieve better target affinity, lower drug dosage to achieve a therapeutic effect, and controlled drug release with improved pharmacokinetics and pharmacodynamics. This article discusses the development of Janus particles for tailored and improved delivery of pharmaceutical agents for diabetes treatment and antimicrobial applications. It provides an account of advances in the synthesis of Janus particles from various materials using different approaches. It appraises Janus particles as a promising particulate system with the potential to improve conventional delivery systems, providing a better loading capacity and targeting specificity whilst promoting multi-drugs loading and single-dose-drug administration.

Aptamer-Mediated Antiviral Approaches for SARS-CoV-2.

2020 and 2021 were disastrous years across the world, with the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) virus as a pandemic, which continues to be a top global health issue. There are still many countries and regions struggling to fight coronavirus disease 2019 (COVID-19), and, with the emergence of the various variants of the virus, we are still far from considering this global pandemic over. In addition to having good diagnostic tools and a variety of vaccines with high efficacy, it is of utmost importance to develop effective antiviral drugs or therapies to battle COVID-19. Aptamers known as the next-generation targeting elements can offer promising opportunities in developing antiviral drugs against SARS-CoV-2. This is owing to their high specificity and affinity, making them ideal for targeting ligands and neutralizers to impede both, viral entry and replication or even further enhance the anti-infection effects in the infected host cells. Also, aptamers are extremely attractive as they can be rapidly synthesized and scalable with a lower production cost. This work provides in-depth discussions on the potential of aptamers in therapeutic applications, their mode of action, and current progress on the use of aptamer-based therapies against SARS-CoV-2 and other viruses. The article also discusses the limitations associated with aptamer-based SARS-CoV-2-antiviral therapy with several proposed ideas to resolve them. Lastly, theranostic applications of aptamer nanoformulated dendrimers against viral infections are discussed.

A Novel Sustainable Process for Multilayer Graphene Synthesis Using CO2 from Ambient Air.

Graphene produced by different methods can present varying physicochemical properties and quality, resulting in a wide range of applications. The implementation of a novel method to synthesize graphene requires characterizations to determine the relevant physicochemical and functional properties for its tailored application. We present a novel method for multilayer graphene synthesis using atmospheric carbon dioxide with characterization. Synthesis begins with carbon dioxide sequestered from air by monoethanolamine dissolution and released into an enclosed vessel. Magnesium is ignited in the presence of the concentrated carbon dioxide, resulting in the formation of graphene flakes. These flakes are separated and enhanced by washing with hydrochloric acid and exfoliation by ammonium sulfate, which is then cycled through a tumble blender and filtrated. Raman spectroscopic characterization, FTIR spectroscopic characterization, XPS spectroscopic characterization, SEM imaging, and TEM imaging indicated that the graphene has fifteen layers with some remnant oxygen-possessing and nitrogen-possessing functional groups. The multilayer graphene flake possessed particle sizes ranging from 2 µm to 80 µm in diameter. BET analysis measured the surface area of the multilayer graphene particles as 330 m2/g, and the pore size distribution indicated about 51% of the pores as having diameters from 0.8 nm to 5 nm. This study demonstrates a novel and scalable method to synthesize multilayer graphene using CO2 from ambient air at 1 g/kWh electricity, potentially allowing for multilayer graphene production by the ton. The approach creates opportunities to synthesize multilayer graphene particles with defined properties through a careful control of the synthesis parameters for tailored applications.

Embelin and Its Derivatives: Design, Synthesis, and Potential Delivery Systems for Cancer Therapy.

Embelin is a naturally occurring benzoquinone that inhibits the growth of cancer cells, making it a potent anticancer drug. However, the low water solubility of embelin restricts its clinical applicability. This review provides a concise summary and in-depth analysis of the published literature on the design and synthesis of embelin derivatives possessing increased aqueous solubility and superior therapeutic efficacy. In addition, the potential of drug delivery systems to improve the anticancer capabilities of embelin and its derivatives is discussed.

Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development.

The spread of coronavirus diseases has resulted in a clarion call to develop potent drugs and vaccines even as different strains appear beyond human prediction. An initial step that is integral to the viral entry into host cells results from an active-targeted interaction of the viral spike (S) proteins and the cell surface receptor, called angiotensin-converting enzyme 2 (ACE2). Thus, engineered ACE2 has been an interesting decoy inhibitor against emerging coronavirus infestation. This article discusses promising innovative ACE2 engineering pathways for current and emerging coronavirus therapeutic development. First, we provide a brief discussion of some ACE2-associated human coronaviruses and their cell invasion mechanism. Then, we describe and contrast the individual spike proteins and ACE2 receptor interactions, highlighting crucial hotspots across the ACE2-associated coronaviruses. Lastly, we address the importance of multivalency in ACE2 nanomedicine engineering and discuss novel approaches to develop and achieve multivalent therapeutic outcomes. Beyond coronaviruses, these approaches will serve as a paradigm to develop new and improved treatment technologies against pathogens that use ACE2 receptor for invasion.

Medical applications of biopolymer nanofibers.

A wide array of biomedical applications, extending from the fabrication of implant materials to targeted drug delivery, can be attributed to polymers. The utilization of chemical monomers to form polymers, such as polypropylene, polystyrene, and polyethylene, can provide high mechanical stability to them and they can be utilized for diverse electronic or thermal applications. However, certain chemical-based synthetic polymers are toxic to humans, animals, plants, and microbial cells. Thus, biopolymers have been introduced as an alternative to make them utilizable for biomedical applications. Even though biopolymers possess beneficial biomedical applications, they are not stable in biological fluids and exhibit toxicity in certain cases. Recent advances in nanotechnology have expanded its applicational significance in various domains, especially in the evolution of biopolymers to transform them into nanoparticles for numerous biomedical applications. In particular, biopolymers are fabricated as nanofibers to enhance their biological properties and to be utilized for exclusive biomedical applications. The aim of this review is to present an overview of various biopolymer nanofibers and their distinct synthesis approaches. In addition, the medical applications of biopolymer nanofibers, including antimicrobial agents, drug delivery systems, biosensor production, tissue engineering, and implant fabrication, are also discussed.

Cancer Diagnostics and Early Detection Using Electrochemical Aptasensors.

The detection of early-stage cancer offers patients the best chance of treatment and could help reduce cancer mortality rates. However, cancer cells or biomarkers are present in extremely small amounts in the early stages of cancer, requiring high-precision quantitative approaches with high sensitivity for accurate detection. With the advantages of simplicity, rapid response, reusability, and a low cost, aptamer-based electrochemical biosensors have received considerable attention as a promising approach for the clinical diagnosis of early-stage cancer. Various methods for developing highly sensitive aptasensors for the early detection of cancers in clinical samples are in progress. In this article, we discuss recent advances in the development of electrochemical aptasensors for the early detection of different cancer biomarkers and cells based on different detection strategies. Clinical applications of the aptasensors and future perspectives are also discussed.

Aptamers as promising nanotheranostic tools in the COVID-19 pandemic era.

The emergence of SARS-COV-2, the causative agent of new coronavirus disease (COVID-19) has become a pandemic threat. Early and precise detection of the virus is vital for effective diagnosis and treatment. Various testing kits and assays, including nucleic acid detection methods, antigen tests, serological tests, and enzyme-linked immunosorbent assay (ELISA), have been implemented or are being explored to detect the virus and/or characterize cellular and antibody responses to the infection. However, these approaches have inherent drawbacks such as nonspecificity, high cost, are characterized by long turnaround times for test results, and can be labor-intensive. Also, the circulating SARS-COV-2 variant of concerns, reduced antibody sensitivity and/or neutralization, and possible antibody-dependent enhancement (ADE) have warranted the search for alternative potent therapeutics. Aptamers, which are single-stranded oligonucleotides, generated artificially by SELEX (Evolution of Ligands by Exponential Enrichment) may offer the capacity to generate high-affinity neutralizers and/or bioprobes for monitoring relevant SARS-COV-2 and COVID-19 biomarkers. This article reviews and discusses the prospects of implementing aptamers for rapid point-of-care detection and treatment of SARS-COV-2. We highlight other SARS-COV-2 targets (N protein, spike protein stem-helix), SELEX augmented with competition assays and in silico technologies for rapid discovery and isolation of theranostic aptamers against COVID-19 and future pandemics. It further provides an overview on site-specific bioconjugation approaches, customizable molecular scaffolding strategies, and nanotechnology platforms to engineer these aptamers into ultrapotent blockers, multivalent therapeutics, and vaccines to boost both humoral and cellular immunity against the virus. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Biosensing Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease.

Green approaches for the synthesis of metal and metal oxide nanoparticles using microbial and plant extracts.

Green synthesis approaches are gaining significance as promising routes for the sustainable preparation of nanoparticles, offering reduced toxicity towards living organisms and the environment. Nanomaterials produced by green synthesis approaches can offer additional benefits, including reduced energy inputs and lower production costs than traditional synthesis, which bodes well for commercial-scale production. The biomolecules and phytochemicals extracted from microbes and plants, respectively, are active compounds that function as reducing and stabilizing agents for the green synthesis of nanoparticles. Microorganisms, such as bacteria, yeasts, fungi, and algae, have been used in nanomaterials' biological synthesis for some time. Furthermore, the use of plants or plant extracts for metal and metal-based hybrid nanoparticle synthesis represents a novel green synthesis approach that has attracted significant research interest. This review discusses various biosynthesis approaches via microbes and plants for the green preparation of metal and metal oxide nanoparticles and provides insights into the molecular aspects of the synthesis mechanisms and biomedical applications. The use of agriculture waste as a potential bioresource for nanoparticle synthesis and biomedical applications of biosynthesized nanoparticles is also discussed.

Synthesis approach-dependent antiviral properties of silver nanoparticles and nanocomposites.

Numerous viral infections are common among humans, and some can lead to death. Even though conventional antiviral agents are beneficial in eliminating viral infections, they may lead to side effects or physiological toxicity. Silver nanoparticles and nanocomposites have been demonstrated to possess inhibitory properties against several pathogenic microbes, including archaea, bacteria, fungi, algae, and viruses. Its pronounced antimicrobial activity against various microbe-mediated diseases potentiates its use in combating viral infections. Notably, the appropriated selection of the synthesis method to fabricate silver nanoparticles is a major factor for consideration as it directly impacts antiviral efficacy, level of toxicity, scalability, and environmental sustainability. Thus, this article presents and discusses various synthesis approaches to produce silver nanoparticles and nanocomposites, providing technological insights into selecting approaches to generate antiviral silver-based nanoparticles. The antiviral mechanism of various formulations of silver nanoparticles and the evaluation of its propensity to combat specific viral infections as a potential antiviral agent are also discussed.

Anti-SARS-CoV-1 and -2 nanobody engineering towards avidity-inspired therapeutics.

In the past two decades, the emergence of coronavirus diseases has been dire distress on both continental and global fronts and has resulted in the search for potent treatment strategies. One crucial challenge in this search is the recurrent mutations in the causative virus spike protein, which lead to viral escape issues. Among the current promising therapeutic discoveries is the use of nanobodies and nanobody-like molecules. While these nanobodies have demonstrated high-affinity interaction with the virus, the unpredictable spike mutations have warranted the need for avidity-inspired therapeutics of potent inhibitors such as nanobodies. This article discusses novel approaches for the design of anti-SARS-CoV-1 and -2 nanobodies to facilitate advanced innovations in treatment technologies. It further discusses molecular interactions and suggests multivalent protein nanotechnology and chemistry approaches to translate mere molecular affinity into avidity.