Biologics, Volume 6, Issue 1 (March 2026) – 9 articles

Background/Objectives: Protein–protein interactions (PPIs) involving oncogenic drivers remain among the most intractable targets in cancer biology due to their dynamic conformations and limited accessibility to conventional small molecules. Although antibodies and inhibitors have achieved clinical success against targets such as PD-1/PD-L1 and MYC, challenges persist related to tissue penetration, intracellular delivery, resistance, and incomplete blockade of key interface hotspots. The objective of this study is to develop an integrated computational framework for systematically designing hotspot-conditioned de novo miniprotein binders to target these interfaces. Methods: We present DesignForge, a computational protein design pipeline that integrates energetic hotspot identification, generative backbone design, sequence optimization, and structural confidence evaluation. The framework combines hotspot mapping using an open force-field-based energetic analysis module with generative backbone sampling using BindCraft, sequence optimization using ProteinMPNN, and structural validation using AlphaFold2. This in silico pipeline was applied to three representative oncogenic interfaces: PD-1/PD-L1, MYC/MAX, and KRAS/RAF. Results: Computationally generated designs exhibited high predicted structural confidence, favorable interface energetics, and consistent engagement of identified hotspot residues across targets. AlphaFold2-Multimer structural modeling indicated that the candidate PD-1 mimetic scaffolds, MYC/MAX interface binders, and KRAS interaction candidates can adopt conformations compatible with the target interfaces. Energetic contact analysis further supported predicted engagement of key hotspot residues. These findings support the computational feasibility of hotspot-conditioned binder generation using a unified design workflow. Conclusions: DesignForge provides a reproducible computational framework for hotspot-guided de novo protein binder design targeting oncogenic protein–protein interfaces. The designs reported here represent computational predictions derived from structural modeling and energetic analysis. Experimental biochemical and cellular validation will be required to determine the functional activity of the proposed binders. Full article

Background: Dextran sodium sulfate (DSS)-induced colitis serves as a preclinical model for studying gut dysbiosis and inflammation relevant to inflammatory bowel disease (IBD) and its long-term complication of colorectal cancer (CRC). Beetroot (Beta vulgaris L.) extract, rich in betalains, polyphenols, and nitrates, exhibits antioxidant and anti-inflammatory properties. This study investigated beetroot extract’s effects on gut microbiota composition and predicted functional pathways in DSS-induced colitis. Methods: Male BALB/c mice were divided into four groups: control (water), DSS-only, beetroot 250 mg/kg + DSS, and beetroot 500 mg/kg + DSS. Beetroot extract was administered orally for 14 days prior to and during DSS exposure. Gut microbial profiles were analyzed using 16S rRNA sequencing, while microbial diversity, community structure, and predicted metabolic functions were evaluated using Shannon, Chao1, PCoA, PERMANOVA, and PICRUSt2 analyses. Results: DSS administration significantly reduced body weight, microbial diversity, and Bacteroidota abundance, while increasing Proteobacteria and Desulfobacterota—a classic colitis-associated dysbiosis signature. Beetroot supplementation restored body weight and microbial balance in a dose-dependent manner, with the 500 mg/kg group showing near-complete normalization of the microbiota. Functional predictions revealed the upregulation of short-chain fatty acid (SCFA) biosynthesis, glutathione metabolism, and amino acid pathways, and suppression of lipopolysaccharide biosynthesis. Identified phytochemicals, including betanin, ferulic acid, and rutin, were associated with antioxidant and prebiotic activities that support microbial restoration. Conclusions: Beetroot extract mitigates DSS-induced gut dysbiosis and inflammation by enhancing microbial diversity, restoring SCFA-associated taxa, and promoting anti-inflammatory and antioxidant pathways. These findings highlight beetroot as a promising natural dietary intervention for colitis and microbiome-associated intestinal disorders. Full article

Background: Cerliponase alfa is an intracerebroventricular (ICV) enzyme replacement therapy (ERT) and the only approved treatment for neuronal ceroid lipofuscinosis type 2 (CLN2) disease. While generally well tolerated, infusion-associated reactions (IARs), including hypersensitivity events and anaphylaxis, remain a recognized safety consideration. Methods: This single-center, retrospective study describes the incidence and management of IARs in pediatric patients with CLN2 receiving long-term ICV cerliponase alfa at Great Ormond Street Hospital, London, United Kingdom. Results: Over a 10-year period (2014–2024), 31 patients received approximately 2705 ICV infusions. Eleven patients experienced at least one IAR. Most reactions were mild and transient, typically consisting of pyrexia, vomiting, or rash, and were managed conservatively with antipyretics and antihistamines. Four patients required steroid intervention following recurrent or more pronounced symptoms, which led to improved infusion tolerance. One patient experienced a single episode of anaphylaxis that required treatment with intramuscular adrenaline and intravenous hydrocortisone. Therapy was continued with a revised pre-medication regime, with no further severe reactions. Conclusions: These findings demonstrate that IARs to ICV cerliponase alfa are typically mild and readily manageable within a multidisciplinary framework. They highlight the importance of structured infusion protocols, vigilant monitoring strategies, and a coordinated management approach to ensure the long-term safety of ERT for children with CLN2 disease. Full article

Background/Objectives: Brucella is a major global One Health threat, causing an estimated 2.1 million human infections and substantial livestock losses annually, with no vaccine currently available for humans, underscoring the urgent need for a safe and effective vaccine. Methods: Employing a reverse vaccinology approach, a novel 175-mer multiepitope vaccine (Mvax) targeting Brucella FrpB was computationally designed in this study, incorporating two B-cell, two MHC class I (MHC-I), and three MHC class II (MHC-II) epitopes selected for their high predicted antigenicity, safety, and IFN-γ-inducing potential. Human β-defensin-3 (hBD3) was fused to the N-terminus as an adjuvant, followed by comprehensive in silico evaluation of the construct. Results: Population coverage analysis predicted 99.59% global MHC class I/II coverage for selected epitopes. In silico analyses predicted that Mvax has high solubility (Protein-SOL score: 0.808), a high antigenicity score (VaxiJen: 1.06), and a negative GRAVY index (−0.881), indicating favorable predicted physicochemical characteristics. iMODS, CABS-Flex 3, and molecular dynamics simulations suggested theoretical stability trends for the modeled vaccine complexes. C-ImmSim immune simulations further predicted elevated Th1 cell populations and associated cytokines (IL-12, IFN-γ, IL-2) following both single and multiple simulated Mvax exposures. Conclusions: The computational analyses described here provide a theoretical modeling basis for an antivirulence multi-epitope vaccine design against human brucellosis, with predicted metrics and simulated immune responses requiring empirical validation. Full article

Interleukin-6 (IL-6) is a multifunctional cytokine with an essential role in immunity, inflammation, and cancer. Produced by immune, stromal and epithelial cells in response to infection or tissue stress, IL-6 regulates immune responses, acute-phase proteins (including serum amyloid A and C-reactive protein), hematopoiesis, and tissue remodeling. These effects are mediated via classical and trans-signaling pathways, which activate key intracellular cascades such as JAK/STAT3, MAPK, and PI3K/AKT. Accumulating evidence implicates dysregulated IL-6 signaling in both oncologic and infectious diseases, where it contributes to disease progression, immune evasion, and therapeutic resistance. This review aims to critically examine the role of IL-6 as a biomarker and therapeutic target in these two major clinical contexts: in cancer, IL-6 levels reflect tumor burden, prognosis, and therapy resistance in both adult and pediatric patients; in infectious diseases, circulating IL-6 may support early diagnosis and risk stratification, particularly in vulnerable pediatric populations. By integrating molecular mechanisms with clinical evidence, this review highlights IL-6 as a unifying biomarker linking inflammation, infection, and malignancy. It also addresses current limitations, including assay variability, lack of standardized reference ranges, especially in children, and challenges in clinical implementation. Full article

Background/Objectives: The rates and predictors of clinical remission, a novel and practical therapeutic goal in severe asthma, have been inconsistently reported across studies. Data on clinical remission in Japanese patients remain limited. The aim of this study was to assess the rate of four-component clinical remission and its predictors in Japanese adult patients with severe asthma. Methods: This retrospective study enrolled adult patients with severe asthma who had initiated biologic therapy at least 12 months prior to inclusion at Nagoya City University Hospital. The primary endpoint was the achievement rate of four-component clinical remission, defined as (1) no maintenance oral corticosteroids (OCS); (2) no exacerbations for 12 months; (3) Asthma Control Test (ACT) score ≥ 20; and (4) forced expiratory volume in one second (FEV₁) ≥ 80% of predicted. The secondary endpoint was to identify factors, including airway structural indices measured using chest computed tomography (CT), associated with clinical remission at 12 months. Results: Among 87 patients with severe asthma, 26 (30%) achieved four-component clinical remission after 12 months of biologic therapy. In univariate analysis, clinical remission was more frequently achieved in patients with chronic rhinosinusitis, higher FEV₁ (% predicted), higher blood eosinophil counts, higher ACT scores, fewer exacerbations in the previous year, higher Lund–Mackay scores, and smaller airway wall thickness and luminal areas on CT (all p < 0.05). Multivariate analysis revealed that higher blood eosinophil counts and fewer exacerbations in the previous year were independently associated with clinical remission (both p < 0.05). Conclusions: After 12 months of biologic therapy, 30% of patients with severe asthma achieved four-component clinical remission. Higher blood eosinophil counts and fewer prior exacerbations were associated with higher remission rates. Full article

The complement system is a key component of innate immunity, responsible for mediating the rapid clearance of pathogens and coordinating adaptive immune responses. Although complement activation is essential for effective infection control and prevention, its excessive or dysregulated function contributes to the pathogenesis of various immune-mediated disorders. Therefore, therapeutic inhibition of the overactive complement cascade, in which specific components are selectively blocked to suppress pathological activation, plays an important role in the treatment of various complement (immune)-mediated diseases. This article provides an overview of complement inhibition as a therapeutic strategy, highlighting the infectious risks associated with its use. Disruption of complement-dependent host defence mechanisms increases the risk of invasive infections (caused by encapsulated pathogens, e.g., Neisseria spp., Streptococcus pneumoniae and Haemophilus influenzae type B), which represent a significant clinical challenge. Therefore, the use of complement inhibition should not only be effective but also safe in combination with the application of all possible tools to prevent infections. Strategies, such as vaccination and antibiotic prophylaxis, are crucial to minimise these complications, despite the persistence of the risk of breakthrough infections. Furthermore, this review examines advancements in patient risk stratification, evaluates alternative preventive measures, and identifies key gaps in current clinical practice. Future directions include improving monitoring protocols, creating more selective or locally acting complement inhibitors, and implementing biomarker-driven personalised therapies that maximise benefits while reducing side effects. Full article

Bone tissue engineering offers a promising alternative to autografts and allografts for treating critical bone defects. Hydrogels, three-dimensional hydrophilic polymer networks, have emerged as leading scaffold materials due to their ability to mimic native extracellular matrix properties while providing tunable biocompatibility, biodegradability, mechanical characteristics, and high water content, enabling nutrient transport and cell viability. These scaffolds can be loaded with bioactive cues, including growth factors, peptides, and nanoparticles, and can deliver stem cells, supporting localised and sustained bone regeneration. Recent advances in hydrogel design have improved osteoinductivity and osteoconductivity through controlled physical, chemical, and mechanical properties, and sophisticated fabrication strategies such as 3D bioprinting and nanostructuring. This review provides a comprehensive overview of hydrogel-based scaffolds for bone tissue engineering, discussing material types, bioactive factor delivery, host tissue interactions, including immune modulation and osteogenic differentiation, and the latest preclinical and clinical applications. Finally, we highlight the remaining challenges and critical design requirements for developing next-generation hydrogels that integrate structural integrity with biological functionality. Full article

The cellular prion protein (PrP^C) displays a functional repertoire that extends well beyond its classical link to transmissible spongiform encephalopathies. Abundant in the nervous system and localized within lipid raft microdomains, PrP^C has emerged as a multifunctional signaling platform that regulates cell differentiation, neurogenesis, neuroprotection, and synaptic plasticity. Recent evidence highlights its dynamic expression in stem cell populations, where it participates in multimolecular complexes that control lineage commitment, particularly during neuronal differentiation. PrP^C expression tightly correlates with stem cell status, making it a promising biomarker of stemness and developmental progression. Through interactions with growth factors, extracellular matrix components, and synaptic proteins, PrP^C functions as a molecular integrator of signals essential for tissue repair and regeneration. Preclinical studies demonstrate that recombinant PrP^C can stimulate neurogenesis and tissue repair, while monoclonal antibodies modulate its physiological and pathological functions. Likewise, cell-based therapies leveraging PrP^C-enriched stem cells or PrP^C-dependent signaling profiles have shown promise in models of neurodegeneration and ischemia. Conversely, dysregulated PrP^C expression has also been observed in solid tumors, where it contributes to cancer cell survival, proliferation, metastasis, and therapy resistance, reinforcing its role as a regulator of cell fate and an oncological target. This review integrates stem cell biology, tissue regeneration, and oncology into a unified framework, offering a novel perspective in which PrP^C emerges as a shared molecular hub governing both physiological repair and pathological tumor behavior, opening previously unrecognized conceptual and translational opportunities. Full article