Current Protein and Peptide Science - Online First
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Artificial Intelligence in Proteins and Peptides: A Comprehensive Overview from Hybrid Modeling to Deep Learning
Authors: Yindan Luo, Jiaxin Cai and Xiaohua NiuAvailable online: 03 October 2025More Less
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Enzymatic Synthesis of β-lactam Antibiotics: From Enzyme Dataset Construction to Action Mechanism and Semi-Rational Design
Authors: Liang Ma, Kaixuan Hu, Wentong Yu, Dongling Hu, Wenqin Luo, Yujie Cao, Shuang Wang, Mengyu Zhang, Li Liang, Gang He and Jianping HuAvailable online: 17 September 2025More Lessβ-lactam Antibiotics (BLA) are characterized by the presence of lactam rings, which are widely used and have a huge market scale. Currently, the production of BLA is primarily achieved through a chemical process, which introduces a large number of toxic compounds, resulting in relatively high environmental costs. As a part of green chemistry, the enzymatic production of BLA is gaining attention because it is non-toxic and pollution-free. This review focuses on industrial enzymes for BLA biosynthesis, which is critical for understanding the reaction process and addressing the deficiencies of low enzyme stability and activity. In this work, a focused dataset of industrial enzymes involved in BLA biosynthesis was constructed, and the structural characteristics of these enzymes were analyzed based on substrate specificity. Subsequently, eight representative enzyme molecules from the database were selected for detailed analyses, particularly focusing on substrate recognition and action mechanisms. Finally, some suggestions for the semi-rational design of enzymes are put forward given the defects existing in BLA biosynthesis. This review not only partially reveals the structure-function relationship of industrial enzyme molecules used in BLA enzymatic synthesis, but also contributes to the semi-rational design of subsequent enzymes, showing certain theoretical significance and application value.
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MmpS5-MmpL5 Transporters Deliver M. tuberculosis Resistance to Bedaquiline (BDQ) and Delamanid (DLM)
Authors: Khaoula Balgouthi, Emel Eker and Manaf AlMatarAvailable online: 09 September 2025More LessIntroductionOne of the earliest illnesses that has been identified is tuberculosis (TB). The largest challenge in managing tuberculosis today is the growing number of individuals infected with TB bacilli, particularly those that are Extensively drug resistant-tuberculosis (XDR-TB) and Multidrug-resistant tuberculosis (MDR-TB). However, by figuring out the resistance's molecular mechanism, Advanced molecular methods may be used to rapidly determine therapy plans. Combining Delamanid (DLM) with Bedaquiline (BDQ), one of the recently authorized medications, indicates that the therapy is effective.
MethodsWe aim to investigate efflux-mediated resistance mechanisms in M. Tuberculosis by using quantitative real-time PCR to assess the expression level of mmpS5 and mmpL5.
ResultsThe median (M) and interquartile range (Iqr) of mmpL5 and mmpS5 expression varied from 5.65 to 9.01 and 7.95 to 10.74, respectively, when resistant strains were compared with sensitive ones. M and Iqr of mmpL5 and mmpS5 expression, however, ranged from 0.08–3.04 and 0.05–1.61 for sensitive strains, correspondingly.
DiscussionOur findings have implications for the development of fast genotypic drug susceptibility testing (DST). Quantitative real-time PCR to measure the expression level of mmpS5 and mmpL5 of baseline and post-baseline isolates is important to track the development of BDQ and DLM resistance.
ConclusionThus, when developing anti-tuberculosis drugs, mycobacterial MmpS5-MmpL5 transporters should be taken into consideration early on, as they are an MDR-efflux system.
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From CASP13 to the Nobel Prize: DeepMind’s AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond
By Jad AbbassAvailable online: 05 September 2025More LessFour years ago, at the 14th Critical Assessment of Structure Prediction (CASP14), John Moult made a historic announcement that the long-standing challenge of Protein Structure Prediction—a problem that had confounded scientists for over five decades—had been “solved” for single protein chains. Supporting this groundbreaking statement was a plot depicting the median Global Distance Test (GDT) across 87 out of 92 domains, where AlphaFold2, developed by DeepMind, achieved an unprecedented score of 92.4. The bar chart not only underscored AlphaFold2’s remarkable performance—standing out prominently among other methods—but also revealed a level of accuracy that exceeded all prior expectations. In the years since this breakthrough, DeepMind's team has made significant strides. The AlphaFold Database now hosts approximately 214 million structures for various model organisms, covering nearly the entire genome. Research continues to explore multiple facets of protein science, including the prediction of multi-chain protein complex structures and the impact of missense mutations on protein function. The open availability of this extensive database and the suite of AlphaFold2 algorithms has catalysed remarkable advancements in protein biology and bioinformatics. This review will begin by revisiting DeepMind's early efforts in CASP13, detailing the architecture and the remarkable progress that led to their breakthrough of AlphaFold2 in CASP14 (2020). It will then delve into two main areas: (1) AlphaFold’s contributions to the scientific community across various fields over the past four years, and (2) the latest improvements, enhancements, and achievements by DeepMind, including AlphaFold3 and the Nobel Prize in Chemistry.
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Evaluation of FOXP3 Exons 2 and 7 Variants in Recurrent Pregnancy Loss among South Indian Women
Authors: Sufaya Jameel, Sourish Sen, Rashmi Bhuwalka, Parveen Jahan and Insaf Ahmed QureshiAvailable online: 05 September 2025More LessIntroductionOne to two percent of women worldwide experience recurrent pregnancy loss (RPL), defined as the loss of two or more consecutive pregnancies before 20 weeks of gestation. Genetic factors, including variations in the FOXP3 gene, have been implicated in the unexplained etiology of RPL. This study aimed to identify and characterize novel genetic variants in exons 2 and 7 of the FOXP3 gene in South Indian women with idiopathic RPL and to analyze their potential impact on protein structure.
Materials and MethodsThis case-control study involved DNA extraction from 300 participants,including 150 recurrent pregnancy loss (RPL)cases and 150 non-recurrent pregnancy loss (NRPL) controls. Polymerase chain reaction (PCR) and Sanger sequencing were used to identify genetic variants. The identified single-nucleotide polymorphisms (SNPs) were analyzed for frequency differences between the RPL and control groups. Additionally, bioinformatics tools were employed to assess the structural impact of the identified mutations on the FOXP3 protein.
ResultsSeven novel single-nucleotide polymorphisms (SNPs) were identified, with four SNPs (-11InsT, 206G>A in exon 2, and 433InsT, 726A>T in exon 7), showing significant frequency variations between RPL and NRPL groups. The modeled structures of FOXP3 apo and mutant proteins displayed similar structural features, including a DNA-binding domain. Molecular dynamics simulation studies revealed comparable stability between the apo and mutant forms of FOXP3.
DiscussionThe identified mutations in the FOXP3 gene can potentially disrupt its critical immune-regulatory functions, leading to impaired immune tolerance during pregnancy, a key factor in the development of RPL. These mutations may alter the activity or stability of regulatory T cells, which are essential for maintaining pregnancy by preventing immune rejection of the fetus.
ConclusionThese findings provide new insights into the genetic underpinnings of idiopathic RPL and underscore the importance of genetic testing for a better understanding of this condition.
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The Emergence of Bioactive Peptides as Anti-diabetic Agents: A Review
Authors: Ramanand, Rohit Singh, Vedpal Singh and Archita KatroliaAvailable online: 02 September 2025More LessA complex condition called diabetes mellitus is characterized by insufficient or resistant insulin production. The incidence of diseases is rising quickly, placing a significant economic, social, and health burden on the modern world. Interventions in nutrition and improved physical activity could make a big difference in controlling this disease. Bioactive peptides obtained from natural sources have been linked to various therapeutic benefits. Several peptides with anti-diabetic potential may lower blood sugar levels, enhance insulin uptake, and inhibit vital enzymes involved in the onset and progression of diabetes. Many bioactive peptides with anti-diabetic properties have been discovered and validated. A more transparent comprehension of the underlying molecular mechanisms of these peptides will aid the development of new peptide-based pharmaceuticals. The objective of this review was to update our understanding of the genesis, structural features, and mechanism of action. The effects of bioactive peptides on vital enzymes and proteins, such as α-glucosidase, α-amylase, glucagon-like peptides, and dipeptidyl peptidase-IV, which are involved in managing glycaemic levels from carbohydrate consumption through blood glucose regulation, were also addressed. The information obtained through this study and industry endeavours should provide a better understanding and evaluation of the prospects of bioactive peptides with anti-diabetic potential for blood glucose level management.
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The Role of Various Autoantibodies and Alpha2-Macroglobulin in Patients with Hashimoto Disease: Does the Presence of Elevated Antibodies Correlate with Alpha 2-Macroglobulin Levels in Hashimoto Disease?
Available online: 25 August 2025More LessIntroductionAutoimmune Thyroiditis (AIT) is caused by defects in the immune system in people with a genetic predisposition to the disease. The most prevalent type of autoimmune thyroiditis is Hashimoto's thyroiditis (HT). The present article reviews the possible relationship between α2-macroglobulin levels and autoantibodies in patients suffering from Hashimoto's disease.
MethodsA total of 170 patients with Hashimoto's disease, categorized into subclinical (96 patients) and manifest (74 patients) forms, were enrolled in the study. The control group comprised 65 individuals without thyroid pathologies or other autoimmune diseases. The levels of α2-macroglobulin and autoantibodies, including both organ-specific and non-organ-specific, were determined in all study participants.
ResultsOrgan-specific antibody and α2-macroglobulin levels were elevated in all patients studied compared to controls. Analysis of organ non-specific antibody levels in patients revealed elevated levels of antibodies to double-stranded (native) DNA in both the subclinical and manifest groups of patients. There were no statistically significant differences in antibody levels to single-stranded (denatured) DNA between the total patient group and the control groups.
DiscussionThe data obtained demonstrated that there is no significant correlation between α2-macroglobulin levels and autoantibody titres, as well as the severity of autoimmune thyroiditis. This finding suggests that α2-macroglobulin may have an unlikely role in the pathogenesis or as a biomarker of disease activity, including in the presence of antibody-dependent cellular damage. Conversely, antibodies directed against double-stranded DNA have exhibited enhanced informativeness and can be regarded as potential markers of the severity of autoimmune thyroid lesions.
ConclusionConsequently, α2-macroglobulin has no diagnostic value as an indicator of autoimmune process exacerbation in Hashimoto's thyroiditis. Conversely, the presence and level of antibodies to double-stranded DNA may offer a means to assess the severity of the disease and should be the focus of further studies as prognostic markers.
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Comprehensive Analysis of Glycosyltransferase-Related Genes Reveals their Prognostic and Therapeutic Implications in Stomach Adenocarcinoma
Authors: Guizhen Lyu and Dongbing LiAvailable online: 13 August 2025More LessIntroductionThis study aimed to investigate the role of glycosyltransferase-related genes (GRGs) in stomach adenocarcinoma (STAD) through bioinformatic analysis and experimental validation, exploring their potential as prognostic and therapeutic biomarkers.
MethodsWe utilized datasets from TCGA-STAD and GSE26901 to establish training and validation cohorts. Prognostic gene signatures were constructed using differentially expressed genes and LASSO regression. Pathway associations were explored via Gene Set Enrichment Analysis (GSEA), and correlations with immune cell infiltration and immune checkpoint genes were analyzed using CIBERSORT, ESTIMATE, and TIDE. Drug sensitivity was assessed using OncoPredict, and GRG expression was confirmed via qRT-PCR.
ResultsWe identified 20 GRGs as prognostic indicators in STAD, with 14 showing abnormal expression. A six-gene signature (B3GAT3, FUT2, GALNT15, GLT8D1, MGAT4C, and ST8SIA6) was constructed, demonstrating AUC values of 0.662, 0.702, and 0.711 in TCGA-STAD for predicting overall survival at 1, 3, and 5 years, respectively. The risk score was significantly associated with reduced survival and identified as an independent prognostic marker. The GRG profile was found to be correlated with immune cell infiltration, immune checkpoint genes, and drug responsiveness.
DiscussionThe study highlights the significance of GRGs in STAD prognosis and potential therapeutic applications. The GRG signature shows promise as a predictive biomarker, with implications for personalized medicine. Limitations include modest AUC values and the need for larger, diverse cohorts for validation. Future work should integrate multi-omics data and explore the roles of GRGs in immune modulation and drug sensitivity.
ConclusionThe GRG profile serves as a prognostic biomarker for STAD, offering new insights into therapeutic approaches and potential applications in other gastrointestinal cancers.
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An In-Depth Study of Circular RNAs Related to Breast Cancer Treatment and their Implications
Authors: Fatima Akram, Zoha Naeem Rana, Ifrah Shabbir, Taseer Fatima and Ikram ul HaqAvailable online: 07 August 2025More LessCircular RNAs, or circRNAs, play a key role in breast cancer biology, directly impacting the diagnosis, prognosis, and treatment of the disease. This review explores the mechanisms, regulatory roles, and functional significance of circRNAs in breast cancer. Overexpressed circRNAs regulate gene expression, cell cycle progression, and drug response in breast cancer. This process is facilitated by the interaction between small RNA molecules (miRNAs) and proteins that can bind to RNA (RBPs), which target the main messenger RNA (mRNA). Consequently, they influence gene expression, cellular proliferation, and drug resistance. Dysregulated circRNA expression contributes to breast cancer progression by promoting tumor aggressiveness and treatment resistance.
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Pharmacological Evaluation of the Combination Therapy of Novel Herbal Mixture in Polycystic Ovary Syndrome
Available online: 01 August 2025More LessIntroductionAn endocrine condition known as Poly-Cystic Ovarian Syndrome (PCOS) makes females of reproductive age more susceptible to insulin resistance, excessive levels of male hormones, and delayed ovulation. It is the main reason that stimulates infertility in females during their reproductive years. Thus, the objective of the present research is to determine whether oleo-gum resins derived from Boswellia serrata and Commiphora myrrh could be beneficial in the treatment of PCOS using a female animal model (Wistar rats) that were administered 1 mg/ kg of letrozole for induction of the disease.
MethodsA combination therapy of Boswellia serrata and Commiphora myrrh was used to study its effect on rat models administered letrozole (1 mg/kg), employed to induce PCOS. OECD Guidelines 407 and 423 were followed for toxicity studies.
ResultsIt was revealed that the polyherbal mixture is nontoxic and safe to use, according to the results. Furthermore, studies have investigated the potential of a combination of oleo-gum resins in the treatment of letrozole-induced PCOS using animal models. According to the information gathered, it was found that the prepared herbal mixture significantly affected the letrozole-induced PCOS rat models. Additionally, it seems to have potential benefits for PCOS-related hormonal and reproductive disorders.
ConclusionThe polyherbal mixture was considered safe for consumption at a dose concentration of under 2000 mg/ kg and can be used for an extended period. Additionally, the polyherbal mixture improved the outcome of the therapy of PCOS in rat models administered with letrozole (1 mg/ kg) employed to induce PCOS.
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Engineering Strategies for Hyaluronan Synthesis: A Review of Enzyme Modifications, Strain Selection, and Molecular Weight Control
Authors: Mortaza Eivazi, Tahereh Ebrahimi, Kamran Hosseini, Leila Abkhooie and Vahideh TarhrizAvailable online: 24 July 2025More LessHyaluronan is a biopolymer with significant biological and commercial importance, particularly due to its applications in medical, cosmetic, and tissue engineering fields. The molecular weight of HA is a key factor that influences its biological function, ranging from anti-inflammatory properties in high-molecular-weight HA to pro-inflammatory effects in low-molecular-weight HA. Recent advancements in protein and strain engineering have enabled precise control of the molecular weight of hyaluronan by manipulating both hyaluronan synthase enzyme variants and the host microbial strains used in hyaluronan production. Strain engineering, through genetic modification and metabolic pathway optimization, enhances the efficiency and yield of hyaluronan with defined molecular properties. Despite progress in industrial-scale hyaluronan production, achieving monodisperse hyaluronan with well-defined molecular weights remains a challenge. This review explores the current breakthroughs in enzyme and strain engineering strategies to optimize hyaluronan synthase enzyme activity and microbial host systems, aiming to produce size-controlled hyaluronan polymers with improved therapeutic efficacy. We discuss the role of specific hyaluronan synthase enzyme mutations and truncations, strain selection, and metabolic engineering, as well as the potential of in vitro cell-free systems for producing hyaluronan with tailored molecular properties for advanced biomedical applications.
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Insects on the Plate: Nutritional Benefits, Health Impacts, and Market Dynamics
Available online: 11 July 2025More LessIntroductionEdible insects are gaining popularity as a sustainable source of proteins, minerals, vitamins, and bioactive compounds. Insects are nutritious, antibacterial, anti-inflammatory, and antioxidant. Modern processing methods, including roasting, drying, fermentation, and hydrolysis, improve the taste, safety, and digestibility of foods derived from insects. This comprehensive review integrates nutritional, bioactive, and technical aspects to explain edible insects as a future food.
ObjectiveThis study examines edible insects as a healthy, sustainable alternative to plant-based diets. It examines their nutritional profile, health advantages, and widespread diet acceptability potential and limitations.
MethodsThis review paper covered the nutritional composition of edible insects, including minerals, fibre, fats, and amino acids. It also evaluated the health benefits of edible insects and chronic disease prevention. Finally, it explored consumer safety and acceptance of edible insects.
ResultsInsects provide proteins, amino acids, vitamin B12, iron, zinc, and calcium. They promote health and reduce cardiovascular disease and cancer risk. Edible insects benefit musclebuilders and older adults since they are excellent sources of protein and amino acids. Their safety, nutritional efficacy, and defined regulatory frameworks were also reported to improve consumer trust and industry development.
DiscussionEdible insects provide high-quality, sustainable protein. This review highlights their high levels of protein, essential amino acids, and bioactive peptides for metabolic health and disease management. Polyphenols, chitin, and antimicrobial peptides are antioxidants, antihypertensives, and immunomodulators. Enzymatic hydrolysis and microencapsulation enhance nutritional bioavailability, safety, and flavor. Edible insects use less area and release fewer pollutants than animals, making them better for the environment. Legal, technological, and awareness initiatives can promote entomophagy worldwide.
ConclusionConsuming insects provides nourishment and leads to good health. They better meet nutritional needs than animal and plant-based diets and supplement protein consumption. Large-scale deployment requires safety and nutritional studies, transparent regulations, and customer acceptance.
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Comprehensive Review of L-Lysine: Chemistry, Occurrence, and Physiological Roles
Available online: 07 July 2025More LessL-lysine, an essential amino acid, is indispensable for numerous biological functions, including protein synthesis, collagen crosslinking, mineral absorption, and carnitine biosynthesis. Its biosynthesis occurs via the Diaminopimelate (DAP) pathway in bacteria and plants and the α-aminoadipate (AAA) pathway in fungi and some archaea. Lysine catabolism primarily involves the saccharopine pathway. Lysine deficiencies can lead to connective tissue disorders, impaired fatty acid metabolism, anemia, and protein-energy malnutrition. Commercial production relies predominantly on microbial fermentation using Corynebacterium glutamicum, with strains enhanced through classical and metabolic engineering approaches. With global production exceeding 1 million tons annually, which is largely dominated by Chinese manufacturers, lysine supplements are readily accessible and exhibit absorption rates comparable to those of dietary protein sources. Beyond its nutritional role, lysine is integral to epigenetic regulation via histone modifications and is implicated in diseases, such as hyperlysinemia and pyridoxine-dependent epilepsies, underscoring its vital role in health maintenance and industrial relevance.
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Siglecs: From Biomodulation to Immunotherapy
Authors: Jia Chen, Yumin Huang, Yafei Wang, Tianlei Sun, Congcong Li, Yuan Feng and Zhenbiao WuAvailable online: 01 July 2025More LessBackgroundSialic acid-binding immunoglobulin-like lectins (Siglecs) are cell-surface immunological receptors predominantly expressed on immune cells such as monocytes, macrophages, and dendritic cells. They play a crucial role in regulating inflammatory processes in various diseases and serve as immunological checkpoints in cancer. Despite several immune checkpoint inhibitors targeting Siglecs having entered clinical trials, the number of Siglec-targeted immunotherapies remains limited.
ObjectiveThis review aims to investigate the contributions of Siglecs in human diseases and explore novel therapeutic strategies targeting the Siglec-sialic acid immunological axis.
MethodsThe authors systematically searched PubMed, Web of Science, and Google Scholar for publications mainly from 2015-2025, using search terms related to Siglecs, tumors, autoimmune diseases, and specific Siglec subtypes (CD169, Siglec2). Studies were included if they examined Siglecs biology, immunomodulation, or immunotherapeutic potential. Studies not directly relevant to Siglecs function/therapeutics and non-peer-reviewed materials (conference abstracts, editorials) were excluded. Screening was done via titles and abstracts with data referenced from research article results, and eligible articles underwent full-text review for final inclusion.
ResultsThe analysis reveals that Siglecs exhibit dual functions, acting as both activators and inhibitors of immune responses. They are implicated in the pathogenesis of various diseases, including cancer, autoimmune disorders, and viral infections. Several Siglec-targeted immunotherapies are currently in clinical trials, demonstrating their potential in disease management. For instance, Siglec15 and Siglec10 have been identified as potential immune checkpoints in cancer, while Siglec2 and Siglec10 play roles in autoimmune diseases like systemic lupus erythematosus (SLE).
ConclusionSiglecs are key immunomodulators that mediate cell-cell and pathogen interactions, playing pivotal roles in human diseases. Further research into their mechanisms and clinical applications is essential to fully harness their therapeutic potential. Targeting Siglecs offers promising avenues for developing novel immunotherapies, particularly in cancer and autoimmune diseases.
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Molecular Degraders: A Comprehensive Review of Small Molecule Induced Protein Degradation Strategies
Available online: 18 June 2025More LessMolecular degraders represent a ground-breaking class of small molecules revolutionizing drug discovery through the selective elimination of disease-causing proteins, including those previously deemed “undruggable.” This review provides a critical analysis of the design and mechanistic intricacies of molecular degraders, encompassing PROTACs, molecular glues, and SNIPERs, with a focus on their reliance on ubiquitin-mediated protein degradation pathways. Key themes include advancements in E3 ligase selection, the principles guiding ternary complex formation, and the role of structural dynamics in optimizing degrader activity and selectivity. The data for this review was collected from various databases such as Science Direct, United States National Library of Medicine (Pubmed), Google Scholar, Elsevier, Springer, and Bentham. Novel findings, such as the development of non-canonical degrader approaches and their preclinical successes, are examined alongside therapeutic applications in oncology, neurodegenerative diseases, and infectious disorders. Challenges, including resistance mechanisms, safety concerns, and pharmacokinetic limitations, are evaluated to provide a holistic perspective. This review not only highlights the transformative potential of molecular degraders but also identifies future directions and critical gaps that could drive innovation in targeted protein degradation and precision medicine.
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Global Trends in Hepatocellular Carcinoma and TGF-β Research: A Bibliometric and Visualization Analysis from 2000 to 2024
Authors: Liu-Lin Yang, Xing Chen, Kai-Ting Huang and Ji-Long WangAvailable online: 13 June 2025More LessBackgroundTransforming growth factor-beta (TGF-β) plays a pivotal role in advanced hepatocellular carcinoma (HCC) by modulating immune responses, inflammatory processes, and epithelial-mesenchymal transition (EMT) in hepatocytes. It has emerged as a key therapeutic target for HCC.
ObjectiveThis study employs bibliometric analysis to examine literature published between 2000 and 2024, aiming to explore the critical roles of TGF-β in HCC and provide a theoretical foundation for future research.
MethodsThis study utilized the Web of Science Core Collection (WoSCC) database to analyze publications from January 1, 2000, to October 16, 2024. Visualization tools such as CiteSpace, VOSviewer, and SCImago Graphica were utilized to assess publication trends, countries, institutions, journals, authors, keywords, and references, identifying hotspots, trends, and the evolution of TGF-β research in the context of HCC.
ResultsThe analysis encompassed 3,026 publications originating from 79 different countries. China was identified as the leading country in publication volume, with Fudan University being the most prolific institution. The journal Hepatology stood out as the leading publication in terms of both the volume of articles and citation influence. Keyword analysis revealed that recent research (2020–2024) has focused on metabolic regulation, the tumor immune microenvironment, and targeted therapies related to the TGF-β signaling pathway in HCC.
ConclusionThis study highlights the publication landscape, research trends, and hotspots of TGF-β-related HCC research from 2000 to 2024, providing valuable insights and a theoretical basis for future studies in this critical field.
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Applications and Prospects of Artificial Intelligence in Proteomics Via Mass Spectrometry: A Review
Authors: Yun Shao, Chenghui Yang, Shenhuan Ni, Mingwei Pang, Xiaojie Liu, Ren Kong and Shan ChangAvailable online: 05 June 2025More LessProteomics holds immense significance in fundamental and applied research in various fields, including life sciences, medicinal sciences, and pharmaceutical sciences. The rapid development of mass spectrometry (MS) technologies has facilitated MS-based proteomics research, which has emerged as one of the primary methods for determining the composition, structures, and functions of proteins. The necessity of processing these complex datasets has increased significantly owing to the growing volume and diversity of MS data pertaining to proteins. Artificial intelligence (AI) possesses powerful data processing abilities, and is being increasingly employed for handling these challenges. In particular, deep learning has been extensively employed in MS-based proteomics research. This review discusses and compares the different AI algorithms developed for various tasks, including the prediction of protein spectra, retention times, peptide sequences, and MS-based protein structure prediction, and highlights their respective strengths and weaknesses. The limitations and future prospects of AI in MS-based proteomics research are additionally discussed herein.
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Phytoconstituents as Potential Therapeutics against Enzymatic Targets for Neurodegenerative Diseases
Authors: Harshita Singh and Veda Prakash PandeyAvailable online: 27 May 2025More LessNeurodegenerative diseases are brought on by the loss of function of nerve cells in the brain or peripheral nervous system and afflict millions of people worldwide. Parkinson's disease and Alzheimer's disease are the two most common neurodegenerative diseases. These neurodegenerative diseases are multi-factorial, progressive, age-related, and influenced by two factors: genetic and environmental. Successful treatment of neurodegenerative diseases is yet a challenging task due to lack of selectivity, toxicity, and the growth of multi-drug-resistant cells to the currently available drugs. Plant-derived, natural secondary metabolites have a significant impact on the research and development of novel medications against neurodegenerative disease. Plant-derived natural products are frequently regarded as safe and relatively safer substitutes for synthetic drugs. The present review deals with the elucidation of plant-derived secondary metabolites, namely alkaloids, flavonoids, and terpenoids, as anti-neurological therapeutics with special reference to various enzymatic targets, such as β-secretase, γ-secretase, α-Secretase, acetylcholinesterase, monoamine oxidase, and phosphodiesterase-4.
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Aquatic BPI/LBPs: A Promising Antimicrobial Peptide Resource for Disease Control in Aquaculture
Authors: Jingxian Sun, Huiqi Deng, Bingyu Ning, Yaoyao Zhan and Yaqing ChangAvailable online: 27 May 2025More LessAquaculture is currently the fastest-growing food supply industry worldwide. Disease control has always been a core concern in the sector of aquaculture. In recent years, the frequency of aquaculture disease outbreaks has increased dramatically due to the continuously increased antibiotic resistance of pathogens. Therefore, it is imperative to find effective antibiotic alternatives for disease control in aquaculture. Bactericidal permeability increasing/lipopolysaccharide binding proteins (BPI/LBPs) are endogenous peptides ubiquitously expressed in aquatic animals that exhibit antimicrobial effects similar to antibiotics. This review presents an overview of current research on BPI/LBPs derived from aquatic animals, the predicted antimicrobial mechanisms of aquatic BPI/LBPs, and the application potential and prospects of aquatic BPI/LBPs as an antimicrobial peptide (AMP) resource. To sum up, the systematic research on aquatic BPI/LBPs may not only enrich AMP resources but also provide new clues for the development of eco-friendly disease control strategies in aquaculture.
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Messenger RNA Nanomedicine: Innovations and Future Directions
Available online: 23 April 2025More LessWith its high potential, mRNA nanomedicine has become one of the transformative frontiers of modern therapeutic strategies for treating and preventing a wide array of diseases. This review article covers recent developments in mRNA nanomedicine and its prospects in terms of innovations in drug delivery systems, stability improvements, and targeted therapeutic applications. The versatility of mRNA means that almost any protein can potentially be encoded into it, making it a powerhouse for vaccines, gene editing, and protein replacement therapies. Recent breakthroughs in nanoparticle technology have significantly enhanced mRNA molecules' delivery efficiency and stability, surmounting previous barriers concerning rapid degradation and immune system activation. It has been developed innovations such as LNPs, polymer-based carriers, and hybrid nanocarriers have been central to the success of targeted delivery and the sustained release of mRNA. This review further underlines the potential of mRNA nanomedicine for oncological, infectious, and genetic diseases by highlighting ongoing clinical trials, emerging therapeutic paradigms, and future directions that lay much emphasis on delivery platform optimization, mRNA stability, and broadening the scope of mRNA nanomedicine therapy. With the power of emerging technologies and solving present challenges, mRNA nanomedicine has a vast potential to revolutionize the future landscape of personalized medicine and targeted therapies.
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