BioChem, Volume 5, Issue 2 (June 2025) – 7 articles

Proteins are structurally and functionally diverse biomacromolecules that serve a variety of essential activities to ensure complex biological homeostasis. The desire to elucidate and enhance these biological functions has been at the forefront of research for many decades. However, generating active proteins via recombinant expression or through chemical total synthesis each has limitations in terms of yield and functionality. Nature has provided a solution to this problem through evolving protein ligases that catalyze the formation of amide bonds between peptides/proteins, which can be exploited by protein engineers to develop robust functional proteins. Here, we summarize the biochemical mechanisms and applications of multiple cysteine-based protein ligases, especially focusing on how they have been utilized for protein therapeutics and engineering, as well as how they inspired chemists to develop efficient methodologies for protein synthesis (e.g., native chemical ligation). Full article

Background/Objectives: N-Myristoyltransferase inhibitors (NMTi) represent a novel antiviral strategy against mammarenaviruses such as Lassa and Junin viruses. The Z matrix protein inhibits viral ribonucleoprotein (vRNP) activity in a dose-dependent manner. Here, we investigated whether Z-mediated vRNP inhibition depends on Z myristoylation or oligomerization. Methods: We used HEK293T cells transfected with wild-type (WT) or G2A-mutated Z constructs in LCMV minigenome (MG) assays. Cells were treated with the NMTi IMP-1088 and the proteasome inhibitor MG132. Z protein expression, vRNP activity, and VLP production were analyzed by immunofluorescence, western blotting, and colocalization analyses. Results: IMP-1088 treatment led to proteasome-mediated degradation of Z, reducing its inhibition of vRNP activity, which was restored by MG132. The non-myristoylated Z G2A mutant retained vRNP inhibitory activity but showed impaired oligomerization and budding capacity. These findings demonstrate that Z-mediated vRNP inhibition is independent of myristoylation and oligomerization. Conclusions: Z myristoylation and oligomerization are not required for its inhibitory vRNP activity. Targeting Z myristoylation with NMTi impairs virus assembly and budding without affecting Z-mediated inhibition of vRNP activity, supporting the development of NMTi as a promising broad-spectrum antiviral strategy against mammarenaviruses. Full article

Oral solid drug delivery continues to be the gold standard in pharmaceutical formulations, owing to its cost-effectiveness, ease of administration, and high patient compliance. Tablets, the most widely used dosage form, are favored for their precise dosing, simplicity, and economic advantages. Among these, controlled release (CR) tablets stand out for their ability to maintain consistent drug levels, enhance therapeutic efficacy, and reduce dosing frequency, thereby improving patient adherence and treatment outcomes. A well-designed CR system ensures a sustained and targeted drug supply, optimizing therapeutic performance while minimizing side effects. This review delves into the latest advancements in CR formulations, with a particular focus on hydrophilic matrix systems, which regulate drug release through mechanisms such as swelling, diffusion, and erosion. These systems rely on a variety of polymers as drug-retarding agents to achieve tailored release profiles. Recent breakthroughs in crystal engineering and polymer science have further enhanced drug solubility and bioavailability, addressing critical challenges associated with poorly soluble drugs. In terms of manufacturing, direct compression has emerged as the most efficient method for producing CR tablets, streamlining production while ensuring consistent drug release. The integration of the Quality by Design framework has been instrumental in optimizing product performance by systematically linking formulation and process variables to patient-centric quality attributes. The advent of cutting-edge technologies such as artificial intelligence and 3D printing is revolutionizing the field of CR formulations. AI enables predictive modeling and data-driven optimization of drug release profiles, while 3D printing facilitates the development of personalized medicines with highly customizable release kinetics. These innovations are paving the way for more precise and patient-specific therapies. However, challenges such as regulatory hurdles, patent constraints, and the need for robust in vivo validation remain significant barriers to the widespread adoption of these advanced technologies. This succinct review underscores the synergistic integration of traditional and emerging strategies in the development of CR matrix tablets. It highlights the potential of hydrophilic and co-crystal matrix systems, particularly those produced via direct compression, to enhance drug bioavailability, improve patient adherence, and deliver superior therapeutic outcomes. By bridging the gap between established practices and innovative approaches, this field is poised to address unmet clinical needs and advance the future of oral drug delivery. Full article

Background/Objectives: Burns are a prevalent health concern that manifest on the skin’s surface or within organs due to various traumas and necessitate prompt intervention. The healing process of the skin involves a sequence of time-dependent events, commencing with the activation of growth factors and culminating in the expression of various genes. To expedite the healing process of burn wounds, there is a need to develop biodegradable materials and new technologies that are compatible with the skin. Methods: In this study, the roles of tilapia (TL, Oreochromis niloticus) fish skin in burn wound treatment processes were investigated. TL or TL-alginate hydrogels (AGTL) were applied to a burn wound created in Sprague Dawley rats for 7 and 14 days. Following the administration of treatment, the levels of hydroxyproline, a critical element in tissue reorganization, along with the gene expression levels of COL1A1, COL3A1, MMP-2, and MMP-9, and the protein expression levels of MMP-2 and MMP-9 were evaluated. Results: Wound closure processes were faster in AGTL-groups compared to TL-groups, and hydroxyproline levels were found to be higher. While the increase in MMP-2 levels was less, the increase in MMP-9 gene and protein levels was greater in the AGTL-group. Concurrently, COL1A1 levels decreased over 14 days, while COL3A1 levels increased in the AGTL-group. Conclusions: Consequently, it was determined that the biological substances in the TL structure, in conjunction with alginate, were effective in the healing and reorganization of the wound tissue. This finding suggests that tilapia may provide a valuable source of insights for future studies aimed at developing effective wound dressings for wound tissues. Full article

Optical coherence tomography (OCT) phantoms are essential tools for calibrating imaging systems, validating diagnostic algorithms, and bridging technological advancements with clinical applications. This review explores the development and application of materials used in OCT phantoms, emphasising their optical, mechanical, and biochemical fidelity to biological tissues. Gelatin-based phantoms (n = 1.35) offer controllable absorbance and scattering, with penetration depths (PDs) of 500–2000 µm and scattering coefficients (SCs) of 5–20 cm⁻¹ but are unstable at room temperature. Silicone phantoms (n = 1.41) are durable and stable, with SCs of 10–15 cm⁻¹, suitable for long-term studies. Polydimethylsiloxane (PDMS) phantoms (n = 1.41) provide manageable optical properties and are used in microfluidic applications. Polyvinyl alcohol (PVA) phantoms (n = 1.48) mimic soft tissue mechanics, with SCs of 5–15 cm⁻¹, but require freeze–thaw cycles. Fibrin phantoms (n = 1.38) simulate blood clotting, with SCs of 5–20 cm⁻¹. Scattering particles like polystyrene (n = 1.57) and titanium dioxide (TiO₂, n = 2.49) offer modifiable properties, while silica microspheres (SiO₂, n = 3.6) and gold nanoshells (n = 2.59) provide customisable optical characteristics. These materials and particles are crucial for simulating biological tissues, enhancing OCT imaging, and developing diagnostic applications. Despite progress, challenges persist in achieving submicron resolution, long-term stability, and cost-effective scalability. Full article

Personalized cancer vaccines are a promising immunotherapy targeting patient-specific tumor neoantigens, yet their design and efficacy remain challenging. Recent advances in artificial intelligence (AI) provide powerful tools to enhance multiple stages of cancer vaccine development. This review systematically evaluates AI applications in personalized cancer vaccine research over the past five years, focusing on four key areas: neoantigen discovery, codon optimization, untranslated region (UTR) sequence generation, and mRNA vaccine design. We examine AI model architectures (e.g., neural networks), datasets (from omics to high-throughput assays), and outcomes in improving vaccine development. In neoantigen discovery, machine learning and deep learning models integrate peptide–MHC binding, antigen processing, and T cell receptor recognition to enhance immunogenic neoantigen identification. For sequence optimization, deep learning models for codon and UTR design improve protein expression and mRNA stability beyond traditional methods. AI-driven strategies also optimize mRNA vaccine constructs and formulations, including secondary structures and nanoparticle delivery systems. We discuss how these AI approaches converge to streamline effective personalized vaccine development, while addressing challenges such as data scarcity, tumor heterogeneity, and model interpretability. By leveraging AI innovations, the future of personalized cancer immunotherapy may see unprecedented improvements in both design efficiency and clinical effectiveness. Full article