Jia Mi¹, Zhikang Liu¹, Chang Li², Jing Wan^1,*

CMES-Computer Modeling in Engineering & Sciences, Vol.145, No.3, pp. 4089-4106, 2025, DOI:10.32604/cmes.2025.074364 - 23 December 2025

Abstract Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies. Despite notable progress, existing computational techniques struggle to represent the interplay between sequence-derived and structure-dependent protein features. To overcome this limitation, we introduce GLM-EP, a unified framework that fuses protein language models with equivariant graph neural networks. By merging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations, GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification. Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional More >

Mujeebu Rehman¹, Qinghua Liu¹, Ali Ghulam², Tariq Ahmad³, Jawad Khan^4,*, Dildar Hussain^5,*, Yeong Hyeon Gu⁵

CMES-Computer Modeling in Engineering & Sciences, Vol.145, No.1, pp. 779-805, 2025, DOI:10.32604/cmes.2025.067412 - 30 October 2025

Abstract Identifying druggable proteins, which are capable of binding therapeutic compounds, remains a critical and resource-intensive challenge in drug discovery. To address this, we propose CEL-IDP (Comparison of Ensemble Learning Methods for Identification of Druggable Proteins), a computational framework combining three feature extraction methods Dipeptide Deviation from Expected Mean (DDE), Enhanced Amino Acid Composition (EAAC), and Enhanced Grouped Amino Acid Composition (EGAAC) with ensemble learning strategies (Bagging, Boosting, Stacking) to classify druggable proteins from sequence data. DDE captures dipeptide frequency deviations, EAAC encodes positional amino acid information, and EGAAC groups residues by physicochemical properties to generate… More >

Ting Wei^1,2,#, Pengli Wei^2,3,#, Yalei Wang^1,2, Yaqiu Mao^2,3, Jian Yan², Xiaotong Hu², Zhenze Qi², Xu Cai², Changkai Jia², Zhiyuan Zhao², Bingkun Li², Min Qiao², Yaxin Zou^2,3, Tingting Yang⁴, Shiyang Sun², Xuesong Feng³, Pengyun Li^2,*, Hongzhou Shang^1,*, Zhibing Zheng²

Oncology Research, Vol.33, No.10, pp. 2981-3006, 2025, DOI:10.32604/or.2025.065123 - 26 September 2025

Abstract Objectives: Immunomodulatory drugs (IMiDs), functioning as molecular glue degraders, have been approved for treating various hematological malignancies; however, the inevitable acquired drug resistance resulting from their skeletal similarity and hematological toxicities poses significant obstacles to their clinical treatment. The study aimed to develop degraders with potent efficiency and low toxicity. Methods: Phenotypic profiling, elaborate structure-activity relationships (SAR), rational drug design and degradation profiles investigations, quantitative proteomics analysis and cell-based functional studies, and pharmacokinetic studies were conducted to develop more potent degraders. Results: This study developed novel CRBN-binding moieties through methylene deletion in lenalidomide’s isoindole core. Lead… More > Graphic Abstract

Akari Fukumoto, Satoru Matsuda^*

Oncology Research, Vol.33, No.9, pp. 2205-2219, 2025, DOI:10.32604/or.2025.062810 - 28 August 2025

Abstract The non-coding RNAs (ncRNAs) are a family of single-stranded RNAs that have become recognized as crucial gene expression regulators in normal and cancer cell biology. The gut microbiota, which consists of several different bacteria, can actively contribute to the regulation of host metabolism, immunity, and inflammation. Roles of ncRNAs and gut microbiota could significantly interact with each other to regulate the growth of various types of cancer. In particular, a causal relationship among ncRNAs, gut microbiota, and immune cells has been shown for their potential importance in the development of breast cancer. Alteration of ncRNA More >

Juan Francisco Zamora Natera^1,*, Mario Felipe González González¹, Javier Vioque², Julio Girón-Calle², Manuel Alaiz²

Phyton-International Journal of Experimental Botany, Vol.94, No.5, pp. 1533-1544, 2025, DOI:10.32604/phyton.2025.064966 - 29 May 2025

Abstract Jarilla caudata Standl. (Caricaceae) is a wild herbaceous plant native to Mexico recognized for its edible fruits. It is considered to be the closest taxonomically species to Carica papaya L. (Caricaceae), whose seeds have good nutritional and functional properties. This study analyzes and compares the seed chemical compositions of J. caudata and C. papaya to study the nutritional and functional potential of J. caudata seeds. The analysis of the proximate composition was based on standard methods. High-performance liquid chromatography was used to determine the free amino acid profile, gas chromatography to quantify the fatty acid content, and inductively coupled plasma–optical… More > Graphic Abstract

JIE ZHONG¹, JUE LIU¹, XING TANG², WENCHAO ZHOU², GUANGMING SONG¹, YUHUAN ZENG¹, XIAODI ZHANG¹, JIANBIN ZHOU¹, JieZhou¹, LU CAO¹, QUNFENG ZHANG^1,*, YUKUN LI^2,*

Oncology Research, Vol.33, No.6, pp. 1335-1346, 2025, DOI:10.32604/or.2025.058760 - 29 May 2025

Abstract The cell cycle is a tightly coupled series of events that enable cells to grow and proliferate. Cyclin-dependent kinases (CDKs) play crucial roles in the cell cycle by enabling cells to transition between different phases when they are activated. Cell cycle proteins enhance the activity of CDKs, while natural CDK inhibitors (CDKIs) suppress them. The cell cycle continues in cycles under normal conditions, but when conditions change, cells halt or terminate the cell cycle. Tumors are tissues that grow out of control, and the mechanisms of various types of tumors are different; however, almost… More > Graphic Abstract

Xiaobing Li^1,2, Yongsheng Liu¹, Limin Wei¹, Li Rao¹, Jingxin Mao^1,*, Xuemei Li^3,*

BIOCELL, Vol.49, No.5, pp. 813-832, 2025, DOI:10.32604/biocell.2025.062124 - 27 May 2025

Abstract Yeast-based models have become a powerful platform in pharmaceutical research, offering significant potential for producing complex drugs, vaccines, and therapeutic agents. While many current drugs were discovered before fully understanding their molecular mechanisms, yeast systems now provide valuable insights for drug discovery and personalized medicine. Recent advancements in genetic engineering, metabolic engineering, and synthetic biology have improved the efficiency and scalability of yeast-based production systems, enabling more sustainable and cost-effective manufacturing processes. This paper reviews the latest developments in yeast-based technologies, focusing on their use as model organisms to study disease mechanisms, identify drug targets,… More >

MOEKA NAKASHIMA, NAOKO SUGA, AKARI FUKUMOTO, SAYURI YOSHIKAWA, SATORU MATSUDA^*

Oncology Research, Vol.33, No.5, pp. 1007-1017, 2025, DOI:10.32604/or.2025.059657 - 18 April 2025

Abstract Malignant tumors are heterogeneous diseases characterized by uncontrolled cell proliferation, invasion, metastasis, and/or recurrence of their malignancies. In particular, cancer stem cells (CSCs) within these tumors might be responsible for the property of invasiveness and/or therapies-resistance. CSCs are a self-renewing, awfully tumorigenic subpopulation of cancer cells, which are notorious for strong chemoresistance and are frequently responsible the aggravated invasion, metastasis, and/or recurrence. Developing targeting therapies against CSCs, therefore, may be deliberated a more encouraging mission for the greater cancer therapy. Innovation for a more potent anti-CSC treatment has been required as soon as possible.… More > Graphic Abstract

Hong Lei¹, Xiaojian Zhou², Antonio Pizzi^3,*, Guanben Du^2,*, Xuedong Xi²

Journal of Renewable Materials, Vol.13, No.2, pp. 199-249, 2025, DOI:10.32604/jrm.2025.02024-0048 - 20 February 2025

Abstract This review is composed of three main parts each of which is written by well-known top specialists that have been, in a way or other, also the main participants of the majority of the developments reported. Thus, after a general part covering the grand lines and more in-depth views of more recent tannin, lignin, carbohydrate and soy bioadhesives, some mix of the other bio raw materials with soy protein and soy flour and some other differently sourced bioadhesives for wood, this review presents a more in-depth part on starch-based wood adhesives and a more in-depth… More > Graphic Abstract

Mukul Mishra¹, Deeba Khan², Sehbanul Islam^1,*

BIOCELL, Vol.49, No.1, pp. 127-147, 2025, DOI:10.32604/biocell.2025.058038 - 24 January 2025

Abstract The COVID-19 pandemic, caused by the newly emerged coronavirus SARS-CoV-2, has resulted in unprecedented global health challenges, including millions of infections and deaths. While the direct effects of the virus are critical, the interplay between SARS-CoV-2 and cellular host factors significantly impacts the replication cycle of the virus and the clinical severity of COVID-19. This review provides a comprehensive analysis of host-pathogen interactions, focusing on the functional roles and regulatory mechanisms of SARS-CoV-2 viral proteins. We systematically review the literature to detail how SARS-CoV-2 engages with host cellular machinery, with a specific emphasis on their More >