{"title":"Advances in immunomodulation: From dietary influence to computational precision.","authors":"Supraja Mohan, Prasanna Kumar Selvam, Karthick Vasudevan","doi":"10.1016/bs.apcsb.2025.10.004","DOIUrl":"10.1016/bs.apcsb.2025.10.004","url":null,"abstract":"<p><p>Immunomodulators are bioactive agents that play a crucial role in modulating immune responses, making them essential for managing autoimmune disorders, infections, and cancers. This chapter provides a thorough examination of immunomodulators, highlighting their clinical importance and therapeutic potential. It begins with an overview of immunomodulators and their applications, followed by a detailed classification into two primary categories: immunosuppressants and immunostimulants. Additionally, the chapter explores the influence of dietary and lifestyle factors on immunomodulation, emphasizing how specific nutritional components can enhance or suppress immune function, ultimately affecting health outcomes. The integration of computational approaches in immunomodulation is discussed, particularly focusing on the interactions between immunomodulators and the gut microbiome. This section underscores the significance of computational modeling and data analytics, including Artificial Intelligence (AI) and Machine Learning (ML), for predicting therapeutic efficacy and optimizing treatment strategies. Challenges and limitations are critically assessed, addressing the complexities of immune system interactions and the variability in individual responses to immunomodulatory therapies. The chapter concludes with future directions in the field, advocating for continued research to fully unlock the potential of immunotherapeutic interventions. This comprehensive review aims to clarify the interplay between dietary factors, computational advancements, and immunological strategies, ultimately contributing to the development of more effective and personalized therapeutic approaches in immunomodulation.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"151 ","pages":"29-44"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikita Goswami, Amit Mishra, Vijay Kumar Prajapati
{"title":"Immunomodulator drugs: Mechanism of action and systemic effects.","authors":"Nikita Goswami, Amit Mishra, Vijay Kumar Prajapati","doi":"10.1016/bs.apcsb.2025.10.006","DOIUrl":"10.1016/bs.apcsb.2025.10.006","url":null,"abstract":"<p><p>Immunomodulatory drugs or immunomodulators have now become mainstream therapeutic medicine in the field of pharmaceutical industry. They represent a unique class of drug products that are natural or synthetic substances, holding tremendous potential to modulate both innate and adaptive immunity, either by boosting or repressing the immune response. Immunomodulators have shown therapeutic benefits in the treatment of various infections, cancer, autoimmune diseases, as well as in organ transplantation. These drugs are classified into two major categories, immunostimulant and immunosuppressant drugs. Immunostimulant drugs can enhance the body's immune system by increasing the activity of lymphocytes and by producing various serum antibodies and cytokines to fight against various infections, tumors, primary or secondary immunodeficiency. In contrast, immunosuppressant drugs are used to suppress or reduce the immune response during organ transplants, chronic inflammation, and in autoimmune diseases such as rheumatoid arthritis, pemphigus, and lupus erythematosus. This chapter provides a cross-sectional perspective on the mechanism of immunostimulatory as well as of immunosuppressive therapeutics and their systemic effects on the human body.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"151 ","pages":"1-28"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Beatrice Campilan, Weston C de Lomba, Madison J Michles, Tianyi Wang, Victoria Chamberlain, Golara Malaki, Ziya L Gokaslan, Margot Martinez-Moreno, Patricia L Zadnik Sullivan
{"title":"Clinical challenges and therapeutic strategies in chordoma: Translating molecular insights into patient care.","authors":"Beatrice Campilan, Weston C de Lomba, Madison J Michles, Tianyi Wang, Victoria Chamberlain, Golara Malaki, Ziya L Gokaslan, Margot Martinez-Moreno, Patricia L Zadnik Sullivan","doi":"10.1016/bs.apcsb.2026.04.004","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.04.004","url":null,"abstract":"<p><p>Chordoma is a rare, locally aggressive bone tumor originating from notochordal remnants. Despite advances in surgical and radiation-based approaches, effective systemic therapies remain limited, and recurrence rates are high. This chapter explores the current clinical landscape of chordoma management with an emphasis on the integration of molecular insights into therapeutic decision-making. In particular, we highlight emerging strategies targeting brachyury and receptor tyrosine kinases, as well as promising immunotherapies, including PD-1/PD-L1 immune checkpoint inhibitors, cancer vaccines, and adoptive cell therapies. We further underscore the pivotal role of institutional and multi-center biobanking efforts in enabling biomarker discovery, enhancing diagnostic accuracy, and facilitating patient prognostication. Alongside these efforts, clinical trial development and public health considerations provide a comprehensive overview of the present scope and future potential of precision medicine in chordoma. By emphasizing the translational potential of molecular profiling together with advances in the clinical, institutional, and public health infrastructures that support its implementation, this chapter outlines a pathway toward more personalized and effective care for patients with chordoma.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"153 ","pages":"285-320"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Small molecular therapeutic targets for neurodegenerative diseases.","authors":"Nagaraj Rangappa, Riddhi Upadhyay, Nathish Lakshman, Sivasamy Ramasamy, Murugan Sevanan, A Justin, Subashchandrabose Chinnathambi","doi":"10.1016/bs.apcsb.2025.10.012","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2025.10.012","url":null,"abstract":"<p><p>Neurodegenerative diseases such as Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis disease are characterized by progressive neuronal loss, protein aggregation, and synaptic dysfunction. These diseases share common pathological mechanisms including oxidative stress, mitochondrial impairment, chronic neuroinflammation, protein misfolding, and epigenetic dysregulation. Current therapies offer only symptomatic relief and fail to halt disease progression. Recent advances in transcriptomics and proteomics have enabled the identification of shared molecular pathways and druggable targets across multiple neurodegenerative diseases. The key targets, such as BDNF-TrkB, TREM2, SIRT1, PINK1-Parkin, GSK-3β, NLRP3, and mTOR have shown promise in preclinical models, offering opportunities for broad-spectrum therapeutic development. Importantly, blood-brain barrier disruption and neuroinflammatory crosstalk exacerbate disease pathology and hinder drug delivery. Innovative strategies involving nanocarriers, gene therapy, and epigenetic modulation are emerging to overcome these barriers. This review highlights the convergence of disease mechanisms, discusses common molecular signatures and therapeutic vulnerabilities, and explores novel small molecular interventions targeting shared pathways mainly in AD and PD. A deeper understanding of aging-associated molecular dysfunction is essential to design sustainable, disease-modifying therapeutics with cross-disease relevance.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"153 ","pages":"135-167"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Santhosh Mudipalli Elavarasu, Insha Asheem, Nihla M, Udhaya Kumar S, R Magesh, Sasikumar K, George Priya Doss C
{"title":"Transcriptomic insights into epigenetic and immunomodulatory roles of nuclear histone genes in bladder cancer: A bioinformatics approach.","authors":"Santhosh Mudipalli Elavarasu, Insha Asheem, Nihla M, Udhaya Kumar S, R Magesh, Sasikumar K, George Priya Doss C","doi":"10.1016/bs.apcsb.2026.01.002","DOIUrl":"10.1016/bs.apcsb.2026.01.002","url":null,"abstract":"<p><p>Bladder cancer (BC) poses a significant global health and economic burden due to its high recurrence rates, progression risks, and the need for lifelong surveillance. Despite advances in diagnosis and treatment, reliable molecular biomarkers for prognosis and therapeutic targeting remain limited. In this study, we used an integrative bioinformatics approach to identify key dysregulated nuclear genes in BC, focusing on histone variants because of their essential role in chromatin organization and gene regulation. Using RNA-seq data, we performed a quality assessment, aligned reads with STAR, and conducted differential expression analysis using DESeq2. A unique gene expression pattern was seen between the cancer and control groups. From the DEGs, nuclear genes were curated using the NCBI Gene database and analysed their network topology via STRING and Cytoscape. MCODE found the complex cluster, and CytoHubba identified key hub genes, notably histone genes HIST1H3D (H3C4), HIST1H4E (H4C5), and HIST1H4B (H4C2). Functional enrichment via clusterProfiler highlighted roles in chromatin assembly, nucleosome organization, and centromeric dynamics. Notably, pathway analysis revealed links to systemic lupus erythematosus (SLE), neutrophil extracellular trap formation, and transcriptional misregulation, suggesting immunomodulatory roles. Kaplan-Meier survival analysis of patient cohorts using the KM-plotter tool revealed that higher expression of HIST1H4E and HIST1H4B was associated with improved survival outcomes. These findings emphasize the epigenetic and immunological roles of nuclear histone genes in BC progression and lay the groundwork for future translational research aimed at diagnostic and therapeutic advancements.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"152 ","pages":"77-101"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148003949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How cargo driven by kinesin motors can pass efficiently through tau islands on microtubules.","authors":"Ping Xie","doi":"10.1016/bs.apcsb.2025.10.027","DOIUrl":"10.1016/bs.apcsb.2025.10.027","url":null,"abstract":"<p><p>Kinesin-1 is a biological molecular motor that can step processively on microtubules toward the plus end to transport cargo in cells. On microtubules tau proteins can assembly into static cohesive envelopes that are also called islands. Upon reaching the tau island boundary, the kinesin-1 motor dissociates rapidly. An interesting but unclear issue is how the cargo can be transported efficiently by kinesin-1 motors to the plus end in the presence of tau islands. Here, the force dependencies of the dynamics of the single kinesin-1 motor in the absence and presence of tau islands are determined theoretically, with which the dynamics of the cargo transport by two kinesin-1 motors connecting to the cargo is studied. The strategy adopted by the kinesin-1 motors to make the cargo pass efficiently through the tau island is explored. Similarly, the cargo transport by two kinesin-3 motors is also studied, showing that the cargo can pass much more efficiently through the tau island. For comparison, the dynamics of the kinesin-1 motor with a large-sized stationary obstacle on the front tubulin is also studied. The theoretical results explain well the conflicting published experimental data showing that after encountering a small-sized obstacle or tau island the kinesin-1 motor can dissociate rapidly whereas after encountering a large-sized obstacle the kinesin-1 motor can pause for a long time.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"150 ","pages":"519-537"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Periyasamy Vijayalakshmi, Asha Monica Alex, Tharmaraj Vairaperumal, Ping-Yen Liu
{"title":"Future of alternative proteins: Blurring the lines between animal- and plant-based.","authors":"Periyasamy Vijayalakshmi, Asha Monica Alex, Tharmaraj Vairaperumal, Ping-Yen Liu","doi":"10.1016/bs.apcsb.2026.08.001","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.08.001","url":null,"abstract":"<p><p>Rising global demand for sustainable, ethical and nutritious foods has driven major advances in alternative proteins. These innovations are at the intersection of plant and animal-derived products, which propels progress in food technology. This review reviews the emerging landscape of alternative proteins and examines how creativity in hybrid products, precision fermentation, and cultivated meat is transforming protein production, dissolving the long-standing boundaries between animal-based and plant-based food systems. Integrated approaches such as plant-based matrices enriched with cultured animal fats aim to replicate the sensory qualities of conventional meat while alleviating ethical and environmental impacts. Precision fermentation now makes it possible to produce animal-identical proteins, such as whey and casein, entirely without animals, thus bridging the divide between conventional and alternative protein categories. This review offer more sustainable options that maintain quality and nutritional value, aligning with the growing expectations of flexitarian consumers. The convergence of plant-based and animal-based protein analogs marks a major turning point in the global protein sector, creating a transformative context in which both sustainability and consumer satisfaction can be advanced. Using cutting-edge scientific tools including tissue engineering, precision fermentation, and powerful insights from structural biology these proteins can be optimized for large-scale production, better flavour and improved texture. In addition, innovations influence environmental outcomes, ethical considerations, and economic systems in the effort to meet the growing worldwide demand for healthy and sustainable food. The integration of plant-based and animal-based technologies represents a critical milestone for the food industry, offering a promising pathway toward a more sustainable and inclusive protein future through diversified alternative protein strategies.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"154 ","pages":"627-653"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lakshmanan Archana Devi, Radhakrishnan Muthezhilan, Sunitha C Mesta, Periyasamy Vijayalakshmi, Anil Kumar Kotermane Mallikarjunappa, Elayaperumal Sumitha
{"title":"The alternative protein transition: Societal impacts and conclusion.","authors":"Lakshmanan Archana Devi, Radhakrishnan Muthezhilan, Sunitha C Mesta, Periyasamy Vijayalakshmi, Anil Kumar Kotermane Mallikarjunappa, Elayaperumal Sumitha","doi":"10.1016/bs.apcsb.2026.08.017","DOIUrl":"10.1016/bs.apcsb.2026.08.017","url":null,"abstract":"<p><p>The global food system is undergoing a significant transformation driven by the emergence of alternative proteins, including plant-based, cultivated, fermentation-derived, and insect-based sources. This transition is motivated by escalating concerns over climate change, resource inefficiency, animal welfare, and the need to ensure food security for a growing population. This review examines the societal impacts of the alternative protein transition, with a focus on its implications for public health, economic systems, cultural practices, and policy frameworks. Alternative proteins present opportunities to reduce greenhouse gas emissions, minimize land and water use, and diversify protein sources, thereby contributing to more sustainable and resilient food systems. At the same time, the transition introduces complex challenges related to consumer acceptance, affordability, regulatory harmonization, and equitable access across different socio-economic groups. The review further explores how this shift may reshape agricultural livelihoods, disrupt traditional livestock industries, and create new markets and employment opportunities within biotechnology and food innovation sectors. Cultural and ethical considerations are also critically evaluated, as dietary habits and food identities influence the pace and extent of adoption. Despite technological advancements and increasing investment, barriers such as high production costs, scalability issues, and regulatory uncertainties remain significant. In conclusion, the alternative protein transition represents a multifaceted paradigm shift with profound societal implications. Strategic collaboration among stakeholders, inclusive policy development, and continued innovation will be essential to maximize benefits while mitigating risks, ensuring that the transition supports sustainable, equitable, and culturally sensitive food systems worldwide.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"154 ","pages":"655-686"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The multifaceted role of antimicrobial peptides in neurodegeneration: Insights from Drosophila and beyond.","authors":"Priyatama Behera, Nagaraj Rangappa, Madhura Chandrashekar, Amit Mishra, Subashchandrabose Chinnathambi, Monalisa Mishra","doi":"10.1016/bs.apcsb.2025.08.003","DOIUrl":"10.1016/bs.apcsb.2025.08.003","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) are tiny proteins essential for innate immunity in various taxa, including mammals and insects. They provide defence against a wide range of pathogens, including bacteria, viruses, fungi, and parasites. Apart from their antimicrobial properties, new studies have revealed the roles of AMPs in brain ageing, neurodegeneration, and neuroinflammation. With an emphasis on their dysregulation in glial and neuronal tissues and their role in neuroinflammation, mitochondrial dysfunction, and neuronal loss, we reviewed the new function of AMPs beyond their antimicrobial activity. Findings from Drosophila models of Huntington's disease, Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, and Ataxia-telangiectasia show that immune pathways, like Toll and immune deficiency, drive persistent or ectopic AMP expression, which is similar to the inflammatory processes seen in human neurodegenerative diseases. Furthermore, the dual function of AMPs as mediators of sterile inflammation and protective immunological agents reveals a universal paradox. The translational relevance of these findings is further supported by comparisons with human AMPs, such as LL-37 and β-defensins. LL-37 and β-defensins levels were found to be increased in the cerebrospinal fluid of patients suffering from meningitis. LL-37 is released from neurons and activates glial cells, boosting the production of inflammatory cytokines and decreasing neuronal survival. This chapter redefines AMPs as not only sentinels of microbial defence but also as important participants in preserving or disturbing brain homeostasis by establishing them as a link between immunity and neurobiology.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"149 ","pages":"419-444"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biosimilars: Antibody and nanobody-based therapeutic approaches towards protein misfolding diseases.","authors":"Subashchandrabose Chinnathambi, Nagaraj Rangappa","doi":"10.1016/bs.apcsb.2025.10.014","DOIUrl":"10.1016/bs.apcsb.2025.10.014","url":null,"abstract":"<p><p>Neurodegenerative diseases, such as Alzheimer's disease, and Parkinson's disease, are characterized by progressive neuronal dysfunction and degeneration. These conditions often share pathological hallmarks such as protein misfolding, oxidative stress, neuroinflammation, and mitochondrial dysfunction. This review focuses on key pathological players like Tau and Amyloid-beta in Alzheimer's disease, highlighting their roles in microtubule destabilization, synaptic dysfunction, and neuronal death. The interplay between oxidative stress and these proteinopathies exacerbates neurodegeneration. Recent advances in therapeutic strategies are also explored, particularly the promise of biosimilars, cost-effective alternatives to biologics, targeting pathological hallmarks in neurodegenerative diseases. Biosimilars targeting Tau and Amyloid-beta in Alzheimer's disease, and alpha-synuclein in Parkinson's disease, hold the potential to improve treatment accessibility and reduce economic burdens. However, their development is still in its early stages. This review underscores the urgent need for innovative, affordable, and globally accessible therapeutic solutions to address the rising burden of neurodegenerative diseases.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"151 ","pages":"157-195"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}