Modares Journal of Biotechnology

Abstract One of the most critical characteristics in the use of enzymes is their stability. Several methods are used to increase the stability of enzymes, including chemical changes, mutations, and stabilizing additives. Organic solvents are toxic, volatile, flammable, and sometimes have destructive environmental effects. Among additives, deep eutectic solvents (DES) are recently used to stabilize many enzymes. Due to their unique properties, such as cheapness, stability, non-volatile, biodegradable, and high dissolving power, these solvents can be a suitable alternative to organic solvents used in industry. For these reasons, in this study, the effect of a glycerol, betaine and its deep eutectic solvent on the activity of transglutaminase was investigated. In addition, the kinetic stability of the enzyme was evaluated in the presence and absence of the solvents. The obtained results showed that the affinity of the enzyme toward its substrate decreased, whereas the kcat value and the overall catalytic efficiency of the enzyme were emhanced in the presence of these liquids. Additionally, thermal stability in the presence of DES increased at 40, 50 and 60 °C compared to aqueous buffers. Overall, the results demonstrate that glycerol-betaine-based deep eutectic solvents can be considered as effective additives for enhancing the catalytic performance and thermal stability of transglutaminase.

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), the causative agent of COVID-19, initiates its life cycle by binding to the angiotensin-converting enzyme 2 (ACE2) receptor. The viral spike protein facilitates this binding, enabling viral entry into host cells. Inhibiting ACE2 could therefore prevent viral entry and mitigate COVID-19 pathogenesis. To identify potential ACE2 inhibitors, we employed a combined computational approach involving pharmacophore modeling, molecular docking, and molecular dynamics simulations. A pharmacophore model was generated and used to screen the ZINC database. Subsequently, molecular docking studies were performed to assess the binding affinity of the selected compounds to the ACE2 active site. Six compounds with binding free energies below -11 kcal/mol and favorable binding orientations were identified as potential ACE2 inhibitors. Molecular dynamics simulations were conducted on the top-ranked compound, ZINC39880968, to validate the docking results. The simulation results were consistent with the docking predictions, further supporting the potential inhibitory activity of this compound. Overall, our findings suggest that ZINC39880968 is a promising candidate for further investigation as a potential therapeutic agent against COVID-19.

Abstract Reverse vaccinology is a computational approach for identifying novel vaccine antigens from pathogen genomes without the need for culture, enabling the prediction of potential immunogenic proteins. By employing bioinformatics, molecular simulations, and 3D modeling, this strategy facilitates the design of multi-epitope and subunit vaccines that elicit stronger immune responses and broader protection. In cancers such as lung, colorectal, breast, pancreatic, and liver malignancies, reverse vaccinology enables the identification of tumor-specific neoantigens and mutations, leading to the development of personalized vaccines. These vaccines have demonstrated the ability to activate T and B cell responses, enhance the production of antitumor cytokines, and inhibit tumor growth. The use of nanocarriers, adjuvants, and specific linkers further improves vaccine efficacy and safety. Molecular docking(It is a computational technique for predicting how a molecule binds to a target site) and simulations with TLR and HLA receptors have confirmed the stability and effectiveness of the designed vaccines. The advantages of this approach include personalized therapy, induction of long-lasting immunological memory, and compatibility with other treatment modalities. However, challenges remain, including optimal epitope selection, accurate prediction of peptide–MHC interactions, and overcoming tumor-induced immune suppression. Integration of machine learning, molecular dynamics, and advanced delivery systems has been proposed as promising strategies to optimize vaccine performance. With ongoing progress in omics sciences and bioinformatics, reverse vaccinology is expected to become a key tool for developing safe, effective, and personalized cancer vaccines, potentially transforming cancer immunotherapy by 2030.

Abstract Protein nanoparticles, as inherently biocompatible,programmable and engineerable carriers, possess great potential for targeted drug delivery, controlled release, and the simultaneous integration of diagnosis and therapy (theranostics). This review introduces the main types of protein nanoparticles, their sources, fabrication methods and stabilization strategies, and highlights their therapeutic, imaging, and theranostic applications, along with the design of next-generation protein-based nanovaccine featuring multivalent, particulate antigen display. The fabrication approaches encompass a wide range of techniques, from classical methods such as desolvation, emulsification, self-assembly, and thermal gelation to advanced strategies including nanospray, electrospray, and Nab technology. Stabilization is achieved through two main routes: covalent crosslinking and physical interactions. The protein sources include animal-derived proteins such as albumin and gelatin, as well as plant-based proteins such as zein. In terms of applications, these nanoparticles have been explored for passive targeting based on the enhanced permeability and retention (EPR) effect and active targeting via specific ligand–receptor interactions and intrinsic gp60/SPARC pathways. They have also been investigated for bioimaging, theranostic systems, and the design of novel protein-based nanovaccine platforms. Evidence indicates that these biocarriers outperform soluble formulations and synthetic carriers in enhancing therapeutic efficacy and reducing systemic toxicity, although challenges such as scalability and production uniformity still persist. Finally, emerging research directions and clinical translation opportunities are highlighted, outlining a promising outlook for the development of personalized therapies and next-generation vaccine designs.

Abstract Introduction: Traditional methods of crack repair in concrete structures are costly and temporary. Bacterial self-healing concrete is proposed as a sustainable solution; however, challenges remain, including the survival of bacteria in concrete's alkaline environment and environmental concerns associated with urea use.
Methods: First, the optimal amount of silica nanoparticles was determined based on compressive strength using experimental design and Statgraphics Centurion software. Bacillus subtilis spores (at a concentration of 3.6 × 109 cells/mL) were encapsulated with nutrients in a sodium silicate gel matrix. Four groups of concrete samples, including a control, a sample containing encapsulated bacteria, a sample containing nanosilica, and a hybrid sample (a combination of bacteria and nanosilica), were prepared in accordance with ASTM C150.
Results: The hybrid sample achieved the highest compressive strength (258 kg/cm²) and modulus of rupture (0.3772 MPa), showing improvements of 8.4% and 4.1% over the control sample, respectively. SEM images showed better structural integrity and the simultaneous presence of nanosilica and bacterial calcium carbonate crystals in the hybrid sample. XRD analysis revealed an increase in the peak intensity of calcium carbonate (at 29.4°) and changes in the peak width at half-height in the hybrid sample, indicating increased crystallinity and enhanced bioremediation activity. Conclusion: The proposed hybrid approach successfully improved bacterial survival, bioremediation efficiency, and mechanical strength of concrete simultaneously. The combination of non-urea resistant spores with microencapsulation in sodium silicate and synergism with nanosilica offers a practical and cost-effective solution for the development of next-generation self-healing concretes

Abstract 1,2,4-Butanetriol is a valuable chemical with wide applications in many fields. Currently, butanetriol is mainly synthesized by chemical methods, which are associated with harsh reaction conditions, poor selectivity, the production of numerous by-products, and environmental pollution. In recent years, the bioproduction of butanetriol has been successfully carried out from inexpensive sugars via biological routes, which have milder conditions and less environmental pollution compared with traditional petrochemical methods. Considering that d-xylose is the second most abundant sugar in nature, its conversion into products can significantly improve the economics of biomass-based processes. Two metabolic pathways of d-xylose phosphorylation (the isomerase pathway, which is mainly found in bacteria, and the oxo-reductive pathway, which is present in fungi) have been well studied. Non-phosphorylation pathways also exist, known as xylose oxidative pathways, and have many advantages over traditional phosphorylation pathways. Metabolic engineering of unconventional host strains using novel gene editing tools based on the Cas9/CRISPR system enables economical and sustainable production of butanetriol from renewable biomass. Significant advances in omics data analysis, along with artificial intelligence and machine learning tools, have become transformative approaches. These advanced tools enable systematic cell design, identification and prioritization of novel metabolic pathways, design of efficient enzymes with high efficiency, and fine-tuning of gene expression in different hosts to achieve maximum butanetriol production. The main objective of this article is to investigate novel and efficient butanetriol biosynthetic pathways in different hosts.

Abstract Histamine accumulation in tuna fish is one of the key indicators of food safety and is influenced by physiological factors and post-harvest conditions. This study investigated the relationship between histamine levels and physical–biological parameters including body length, body weight, body temperature, and muscle pH in two tuna species, Euthynnus affinis and Thunnus tonggol. Seasonal sampling was conducted on freshly caught fish from the Persian Gulf, and histamine concentrations were determined using the HPLC method. Statistical analysis revealed that body temperature plays a decisive role in histamine formation; in T. tonggol, an increase in body temperature was significantly associated with higher histamine levels, whereas in E. affinis, the correlation was positive but not statistically significant. Other physiological factors—such as body length, weight, and muscle pH were not reliable predictors of histamine accumulation. These findings indicate that body size has only a minor direct effect on histamine formation, while body temperature and post-harvest conditions are the primary determinants. Therefore, precise temperature management and maintenance of the cold chain after harvesting are essential for controlling histamine levels and enhancing food safety in tuna species.

Abstract Targeted delivery of nucleic acids and drugs to diseased cells remains a major challenge in cancer therapy. This study focuses on Fe3O4/Chitosan/PCL/PEG-HA (PCFPH) nanoparticles designed to enhance PTX and siRNA delivery to HS-578T cells. Characterization by Fourier transform infrared spectroscopy (FTIR), zeta potential, dynamic light scattering (DLS), and scanning electron microscopy (SEM) confirmed the successful synthesis and structural properties suitable for drug and gene loading. The nanoparticles were measured to be approximately 230 nm with a zeta potential of -2.5 mV. Drug and gene release studies at pH=7.4 showed that the release of PTX and siRNA-FAM was controlled and biphasic. Electrophoretic analysis showed that the micellar coating protected these agents from plasma degradation. Cytotoxicity evaluation using MTT assay showed low toxicity (IC50= 492.7 μg/mL) of PCFPH nanocapsules for HS-578T cell line. Agarose gel and fluorescence microscopy results confirmed the superior gene delivery efficiency of PCFPH/siRNA-FAM nanocapsules compared to the control group, due to their stability and the presence of hyaluronic acid groups. This study presents the first application of these nanoparticles for gene and drug delivery.