Protein-quantum dot nanohybrids for bioanalytical applications

A one-step route for the conversion of Cd waste into CdS quantum dots by Acidithiobacillus sp. via unique biosynthesis pathways

Microorganisms serve as biological factories for the synthesis of nanomaterials such as CdS quantum dots. Based on the uniqueness of Acidithiobacillus sp., a one-step route was explored to directly convert cadmium waste into CdS QDs using these bacteria. First, an exhaustive study was conducted to reveal the specific pathways involved in the biosynthesis of CdS QDs. The widely known homologous enzyme, cysteine desulfhydrase, which catalyzes the synthesis of CdS QDs from a cysteine substrate, is also present in Acidithiobacillus sp. and is referred to as the OSH enzyme. The structure of the OSH enzyme was determined through X-ray crystallography. Moreover, we identified two new pathways. One involved the SQR enzyme in Acidithiobacillus sp., which catalyzed the formation of sulfur globules and subsequently catalyzed further reactions with GSH to release H2S; subsequently, a CdS QD biosynthesis pathway was successfully constructed. The other pathway involved extracellular polyphosphate, a bacterial metabolic product, which with the addition of GSH and Cd2+, resulted in the formation of water-soluble fluorescent CdS QDs in the supernatant. Based on the above-described mechanism, after the bioleaching of Cd2+ from cadmium waste by Acidithiobacillus sp., CdS QDs were directly obtained from the bacterial culture supernatants. This work provides important insights into cleaner production and cadmium bioremediation with potential industrial applications.

Rationally designed catalytic nanoplatform for enhanced chemoimmunotherapy via deploying endogenous plus exogenous copper and remodeling tumor microenvironment

Chemodynamic therapy represents a novel tumor therapeutic modality via triggering catalytic reactions in tumors to yield highly toxic reactive oxygen species (ROS). Nevertheless, low efficiency catalytic ability, potential systemic toxicity and inefficient tumor targeting, have hindered the efficacy of chemodynamic therapy. Herein, a rationally designed catalytic nanoplatform, composed of folate acid conjugated liposomes loaded with copper peroxide (CP) and chloroquine (CQ; a clinical drug) (denoted as CC@LPF), could power maximal tumor cytotoxicity, mechanistically via maneuvering endogenous and exogenous copper for a highly efficient catalytic reaction. Despite a massive autophagosome accumulation elicited by CP-powered autophagic initiation and CQ-induced autolysosomal blockage, the robust ROS, but not aberrant autophagy, underlies the synergistic tumor inhibition. Otherwise, this combined mode also elicits an early onset, above all, long-term high-level existence of immunogenic cell death markers, associated with ROS and aberrant autophagy -triggered endoplasmic reticulum stress. Besides, CC@LPF, with tumor targeting capability and selective tumor cytotoxicity, could elicit intratumor dendritic cells (mainly attributed to CQ) and tumor infiltrating CD8+ T cells, upon combining with PD-L1 therapeutic antibody, further induce significant anti-tumor effect. Collectively, the rationally designed nanoplatform, CC@LPF, could enhance tumor chemoimmunotherapy via deploying endogenous plus exogenous copper and remodeling tumor microenvironment.

B-Cell-Epitope-Based Fluorescent Quantum Dot Biosensors for SARS-CoV-2 Enable Highly Sensitive COVID-19 Antibody Detection

A new antibody diagnostic assay with more rapid and robust properties is demanded to quantitatively evaluate anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity in a large population. Here, we developed a nanometer-scale fluorescent biosensor system consisting of CdSe-ZnS quantum dots (QDs) coupled with the highly sensitive B-cell epitopes of SARS-CoV-2 that could remarkably identify the corresponding antibody with a detection limit of 100 pM. Intriguingly, we found that fluorescence quenching of QDs was stimulated more obviously when coupled with peptides than the corresponding proteins, indicating that the energy transfer between QDs and peptides was more effective. Compared to the traditional enzyme-linked immunosorbent assay (ELISA), the B-cell-epitope-based QD-biosensor could robustly distinguish coronavirus disease 2019 (COVID-19) antibody-positive patients from uninfected individuals with a higher sensitivity (92.3–98.1% positive rates by QD-biosensor vs. 78.3–83.1% positive rates by ELISAs in 207 COVID-19 patients’ sera) in a more rapid (5 min) and labor-saving manner. Taken together, the ‘QD-peptides’ biosensor provided a novel real-time, quantitative, and high-throughput method for clinical diagnosis and home-use tests.

Biomolecular Surface Functionalization and Stabilization Method to Fabricate Quantum Dots Nanobeads for Accurate Biosensing Detection

The surface functionalization of quantum dots (QDs) is essential for their application as a label material in a biological field. Here, a protein surface functionalization approach was introduced to combine with silica encapsulation for the sustainable and stable synthesis of QDs nanobeads for biomarker detection. The formation of QDs nanobeads was achieved by multiple mercapto groups in bovine serum albumin (BSA) macromolecules as multidentate ligands to replace hydrophobic ligands on the surface of QDs and decompression. The resulting QDs nanobeads exhibited 20 times more photoluminescence than the corresponding hydrophobic QDs and presented excellent stability under physiological conditions due to the protection of BSA and silica. The nanobeads served as a robust signal-generating reagent to construct the lateral flow immunoassay (LFIA) biosensor for the detection of glycosylated hemoglobin (HbA1c). The concentration of HbA1c was determined within 10 min with high specificity using only 60 μL of whole blood samples collected clinically. The nanobeads-based LFIA biosensor exhibited linear detection of HbA1c from 4.2% to 13.6%. The accuracy and stability of this approach in clinical utility was demonstrated by the detection of HbA1c after a long-term storage of test strips. This protein surface modification technology provides a new way for improving the biological properties of QDs in clinical diagnosis.

Engineered Repeat Protein Hybrids: The New Horizon for Biologic Medicines and Diagnostic Tools

ConspectusThe last decades have witnessed unprecedented scientific breakthroughs in all the fields of knowledge, from basic sciences to translational research, resulting in the drastic improvement of the lifespan and overall quality of life. However, despite these great advances, the treatment and diagnosis of some diseases remain a challenge. Inspired by nature, scientists have been exploring biomolecules and their derivatives as novel therapeutic/diagnostic agents. Among biomolecules, proteins raise much interest due to their high versatility, biocompatibility, and biodegradability.Protein binders (binders) are proteins that bind other proteins, in certain cases, inhibiting or modulating their action. Given their therapeutic potential, binders are emerging as the next generation of biopharmaceuticals. The most well-known example of binders are antibodies, and inspired by them researchers have developed alternative binders using protein design approaches. Protein design can be based on naturally occurring proteins in which, by means of rational design or combinatorial approaches, new binding interfaces can be engineered to obtain specific functions or based on de novo proteins emerging from state-of-the-art computational methodologies.Among the novel designed proteins, a class of engineered repeat proteins, the consensus tetratricopeptide repeat (CTPR) proteins, stand out due to their stability and robustness. The CTPR unit is a helix-turn-helix motif constituted of 34 amino acids, of which only 8 are essential to ensure correct folding of the structure. The small number of conserved residues of CTPR proteins leaves plenty of freedom for functional mutations, making them a base scaffold that can be easily and reproducibly tailored to endow desired functions to the protein. For example, the introduction of metal-binding residues (e.g., histidines, cysteines) drives the coordination of metal ions and the subsequent formation of nanomaterials. Additionally, the CTPR unit can be conjugated with other peptides/proteins or repeated in tandem to encode larger CTPR proteins with superhelical structures. These properties allow for the design of both binder and nanomaterial-coordination modules as well as their combination within the same molecule, making the CTPR proteins, as we have demonstrated in several recent examples, the ideal platform to develop protein-nanomaterial hybrids. Generally, the fusion of two distinct materials exploits the best properties of each; however, in protein-nanomaterial hybrids, the fusion takes on a new dimension as new properties arise.These hybrids have ushered the use of protein-based nanomaterials as biopharmaceuticals beyond their original therapeutic scope and paved the way for their use as theranostic agents. Despite several reports of protein-stabilized nanomaterials found in the literature, these systems offer limited control in the synthesis and properties of the grown nanomaterials, as the protein acts just as a stabilizing agent with no significant functional contribution. Therefore, the rational design of protein-based nanomaterials as true theranostic agents is still incipient. In this context, CTPR proteins have emerged as promising scaffolds to hold simultaneously therapeutic and diagnostic functions through protein engineering, as it has been recently demonstrated in pioneering in vitro and in vivo examples.

Protein-Based Artificial Nanosystems in Cancer Therapy

Proteins, like actors, play different roles in specific applications. In the past decade, significant achievements have been made in protein-engineered biomedicine for cancer therapy. Certain proteins such as human serum albumin, working as carriers for drug/photosensitizer delivery, have entered clinical use due to their long half-life, biocompatibility, biodegradability, and inherent nonimmunogenicity. Proteins with catalytic abilities are promising as adjuvant agents for other therapeutic modalities or as anticancer drugs themselves. These catalytic proteins are usually defined as enzymes with high biological activity and substrate specificity. However, clinical applications of these kinds of proteins remain rare due to protease-induced denaturation and weak cellular permeability. Based on the characteristics of different proteins, tailor-made protein-based nanosystems could make up for their individual deficiencies. Therefore, elaborately designed protein-based nanosystems, where proteins serve as drug carriers, adjuvant agents, or therapeutic drugs to make full use of their intrinsic advantages in cancer therapy, are reviewed. Up-to-date progress on research in the field of protein-based nanomedicine is provided.

Subnanomolar FRET-Based DNA Assay Using Thermally Stable Phosphorothioated DNA-Functionalized Quantum Dots

Quantum dots (QDs) can serve as an attractive Förster resonance energy transfer (FRET) donor for DNA assay due to their excellent optical properties. However, the specificity and sensitivity of QD-based FRET analysis are prominently reduced by nonspecific DNA adsorption and poor colloidal stability during DNA hybridization, which hinders the practical applications of QDs as a biosensing platform. Here, we report subnanomolar FRET assay of DNA through the stabilization of DNA/QD interface using DNA-functionalized QDs with phosphorothioated single-stranded DNA (pt-ssDNA) as a multivalent ligand in an aqueous solution. In situ DNA functionalization was achieved during the aqueous synthesis of CdTe/CdS QDs, resulting in the maximum photoluminescence quantum yields of 76.9% at an emission wavelength of 732 nm. Conventional monothiolated ssDNA-capped QDs exhibited particle aggregation and photoluminescence (PL) quenching during DNA hybridization at 70 °C due to the dissociation of surface ligands. Such colloidal instability induced the nonspecific adsorption of DNA, resulting in false-positive signal and decreased sensitivity with the limit of detection (LOD) of 16.1 nM. In contrast, the pt-ssDNA-functionalized QDs maintained their colloidal stability and PL properties at elevated temperatures. The LOD of the pt-ssDNA-functionalized QDs was >30 times lower (0.47 nM) while maintaining the high specificity to a target sequence because the strong multivalent binding of pt-ssDNA to the surface of QDs prevents the detachment of pt-ssDNA and nonspecific adsorption of DNA. The study suggests that the ligand design to stabilize the surface of QDs in an aqueous milieu is critically important for the high performance of QDs for specific DNA assay.

Mathematical Modeling of Bioassays

The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.

Comparative Analysis of Methods for Enhancement of the Photostability of CdTe@TGA QD Colloid Solutions

The employment of colloid quantum dots in a number of applications is limited by their instability under light irradiation. Additional methods of photostability enhancement of UV+visible-irradiated TGA-stabilized CdTe quantum dots are investigated. Photostability enhancement was observed via either addition of sodium sulphite in the role of chemical oxygen absorber or addition of 1% gelatin, or, finally, by additional stabilization by bovine serum albumine (BSA). The latter method is the most promising, since it not only enhances the quantum dots' photostability but also makes them more biocompatible and extends the possibilities of their biological applications.