Structure-guided design of a trivalent nanobody cluster targeting SARS-CoV-2 spike protein

Development of a nanobody-based immunoassay for the analysis of the disinfectant triclosan in water

Triclosan (TCS), a broad-spectrum antimicrobial agent in pharmaceuticals and personal care products, necessitates environmental monitoring due to its antimicrobial properties and widespread in the environment. In this study, two anti-TCS single-domain antibodies (i.e., nanobodies, Nbs), T1 and T2, were isolated from a phage-displayed Nb library derived from a camel immunized with a mixture of TCS immunogens. The T1-based enzyme-linked immunosorbent assay (ELISA) exhibited a better sensitivity to TCS than the T2-base ELISA. Motivation at enhancing specificity, sensitivity, and stability of Nb-based immunoassays promoted exploring use of a bivalent strategy to enhance performance. The bivalent Nb T1-T1 was tandemized via a linker-(GGGGS)3- between. The thermal stability of the bivalent Nb was improved in comparison with that of a monovalent Nb. The sensitivity of T1-T1-based ELISA, with an IC50 value of 4.3 ng mL-1 of TCS, was improved approximately 2-3 fold in comparison to those of T1-or T2-based ELISAs (8.5 and 14.6 ng mL-1, respectively). The average recovery of TCS from water samples measured with T1-T1-based ELISA was in the range of 99-125 %, which correlated well with that measured by a high-performance liquid chromatography (HPLC) method (R2 > 0.99). TCS in river water samples was detected by the resultant ELISA and an HPLC method, showing a satisfactory correlation.

Synergistic effect of horizontal transfer of antibiotic resistance genes between bacteria exposed to microplastics and per/polyfluoroalkyl substances: An explanation from theoretical methods

Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Molecular dynamics simulations and machine learning can accurately capture the complex interactions between molecules. This study utilized them to identify the HGT risk between bacteria under MPs and PFASs stress. This study found that MPs and PFASs significantly increase the HGT risk between bacteria, up to 1.57 and 1.59 times, respectively. Notably, long-chain PFASs and perfluoroalkyl carboxylic acids increased the HGT risk by 1.38 and 1.40 times, respectively. Additionally, MPs primarily increase the HGT risk by enhancing hydrogen bonding interaction between key proteins in the HGT pathway and "active codons". The electronegativity and polarizability of PFASs critically influence the HGT risk, acting inversely and directly proportional, respectively. The HGT risk between bacteria under the combined stress from PP-MPs and PFASs exhibits a significant synergistic effect (synergistic effect value of 27.6), which markedly increases the HGT risk. Further analysis revealed that a smaller minimum distance and sharper RDF curve peaks between key proteins and "active codons" indicate higher HGT risk. This indicates that stronger interactions lead to higher HGT risk. This study identifies the characteristics of HGT risks between bacteria in aquatic environments under the individual and combined stresses from MPs and PFASs at the molecular level. It provides a theoretical basis for mitigating ARG transfer and comprehensively assessing the health risks posed by these emerging pollutants.

Co-exposure of TMPs and antibiotics in zebrafish: The influence of additives on the risk of hepatotoxicity

Co-exposure of tire microplastics (TMPs) and antibiotics has been confirmed to pose toxic risks to aquatic organisms. However, the contributions of TMP additives to these risks and the underlying mechanisms remain underreported. In this study, factor analysis and molecular docking and molecular dynamics simulations were employed to investigate the differential additive-related hepatotoxicity risks associated with TMP-antibiotic exposure in zebrafish. The differential hepatotoxicity risks of five types of TMPs and six antibiotics were simulated in the presence of additives. Zebrafish exposed to different TMPs showed significant differences in hepatotoxicity risks, with styrene-butadiene rubber (SBR) exhibiting the most pronounced toxic effects. The additive contribution analysis revealed that in the presence of SBR additives, TMPs-antibiotics posed higher toxicity risks to the cytochrome P 17A2 (CYP17A2) isoenzymes CYP2K19, CYP1A, CYP3A65, and CYP2K22 in zebrafish, showing synergistic effects primarily driven by plasticizers. Furthermore, the hepatotoxicity risks of TMPs-antibiotics in zebrafish in the presence of additives were significantly mitigated by the selection of alternative plasticizers. The micromechanisms by which additives affected the TMP-antibiotic hepatotoxicity risks in zebrafish were elucidated through mechanistic analysis. This study aimed to characterize the additive-influenced hepatotoxicity risks of TMPs-antibiotics, providing micro-level insights and theoretical support for ecological risk assessments in aquatic environments.

Improved microbial-plant soil bioremediation of PAHs and heavy metal through in silico methods

The combined pollution of polycyclic aromatic hydrocarbons (PAHs) and organic cadmium (Cd) in farmland soils, and the field controlling strategy need to be studied urgently. In this study, 5 PAHs, 5 Cd and 11 soil conditioners were selected to explore the co-exposure risk and remediation efficiency. Firstly, a significant combination Fl-alkylalkoxy cadmium was obtained using forward and reverse methods coupling variation coefficient methods (the combined pollution value was 0.173). Secondly, the interaction energy of microbial degradation / plant absorption of Fl under Cd stress, and microbial mineralization / plant absorption of alkylalkoxy cadmium under PAHs stress were characterized using factorial experimental design, molecular docking and molecular dynamics simulation. The combined pollution of alkylalkoxy cadmium and dialkyl cadmium, phenanthrene and Benzo [a] pyrene was significant (synergistic contribution rates were 17.58 % and 19.22 %, respectively). In addition, 6 soil conditioners with significant efficiency were selected to design Taguchi orthogonal experimental schemes, indicating the microbial degradation / mineralization and plant absorption were significantly effective (the maximum increase of remediation efficiency was 93.81 %) under the combinations (i.e., trratone, coumarol, fulvamic acid, potassium fertilizer and others, etc.). Finally, it was found that the soil conditioners affected the hydrophobic groups and forces, and the efficiency was proportional to the highest peak value and minimum distance in the RDF curve. This study identifies the risk characteristics of co-exposure of PAHs and Cd and screens effective soil conditioners, providing theoretical guidance for risk controlling.

A single-domain antibody library based on a stability-engineered human VH3 scaffold

Using conventional immunoglobulin G (IgG) molecules as therapeutic agents presents several well-known disadvantages owing to their large size and structural complexity, negatively impacting development and production efficiency. Single-domain antibodies (sdAbs) are the smallest functional antibody format (~ 15 kDa) and represent a viable alternative to IgG in many applications. However, unlike natural single-domain antibodies, such as camelid VHH, the variable domains of conventional antibodies show poor physicochemical properties when expressed as sdAbs. This report identified stable sdAb variants of human VH3-23 from a framework region 2-randomized human VH library by phage display selection under thermal challenge. Synthetic complementarity determining region diversity was introduced to one of the selected variants with high thermal stability, expression level, and monomeric content to construct a human VH sdAb library. The library was validated by panning against a panel of antigens, and target-specific binders were identified and characterized for their affinity and biophysical properties. The results of this study suggest that a synthetic sdAb library based on a stability-engineered human VH scaffold could be a facile source of high-quality sdAb for many practical applications.

Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e

Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.

Next generation single-domain antibodies against respiratory zoonotic RNA viruses

The global impact of zoonotic viral outbreaks underscores the pressing need for innovative antiviral strategies, particularly against respiratory zoonotic RNA viruses. These viruses possess a high potential to trigger future epidemics and pandemics due to their high mutation rate, broad host range and efficient spread through airborne transmission. Recent pandemics caused by coronaviruses and influenza A viruses underscore the importance of developing targeted antiviral strategies. Single-domain antibodies (sdAbs), originating from camelids, also known as nanobodies or VHHs (Variable Heavy domain of Heavy chain antibodies), have emerged as promising tools to combat current and impending zoonotic viral threats. Their unique structure, coupled with attributes like robustness, compact size, and cost-effectiveness, positions them as strong alternatives to traditional monoclonal antibodies. This review describes the pivotal role of sdAbs in combating respiratory zoonotic viruses, with a primary focus on enhancing sdAb antiviral potency through optimization techniques and diverse administration strategies. We discuss both the promises and challenges within this dynamically growing field.

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.