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Prince C, Georgiadou D, Machatti M, Hermann M, van Puijenbroek E. Optimizing asymmetric antibody purification: a semi-automated process and its digital integration. MAbs 2025; 17:2467388. [PMID: 40032656 PMCID: PMC11916402 DOI: 10.1080/19420862.2025.2467388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 02/07/2025] [Accepted: 02/10/2025] [Indexed: 03/05/2025] Open
Abstract
Over the past decades, immunization and display technologies have considerably increased the potential for generating new binders against cell surface targets. Concomitantly, the complexity of biologic therapeutic drugs has also increased, with new asymmetric formats such as bispecific antibodies or antibody fusion proteins making the supply of molecules for preclinical drug discovery more challenging. The purification of those molecules is crucial, and an efficient purification platform for drug discovery research units should have multiple aims. First, it needs to deliver the highest quality proteins for research activities at a fast pace in order to increase screening capacities. Second, it has to deliver protein with sufficient yield in order to cover the project requirements and minimize the repetition of production cycles. Through a case study for a bispecific antibody, we describe a semi-automated and digitalized purification platform aiming at accelerating and optimizing the supply of asymmetric antibodies for drug discovery. We show how the automation of repetitive tasks and the digitalization of the process can lead to increased throughput in the context of complex purifications, including a cation exchange chromatography separation step. Furthermore, we highlight how process digitalization leads to enhanced data capture and accessibility, facilitating decision-making along the purification process. With a maximal throughput of 36 asymmetric antibodies per week and data proving the consistency of the quality delivered, this platform represents a step forward in the supply of complex antibody formats for preclinical drug discovery.
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Affiliation(s)
- Christophe Prince
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Despoina Georgiadou
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Manuela Machatti
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Matthias Hermann
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Erwin van Puijenbroek
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
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2
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Paul JK, Malik A, Azmal M, Gulzar T, Afghan MTR, Talukder OF, Shahzadi S, Ghosh A. Advancing Alzheimer's Therapy: Computational strategies and treatment innovations. IBRO Neurosci Rep 2025; 18:270-282. [PMID: 39995567 PMCID: PMC11849200 DOI: 10.1016/j.ibneur.2025.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 01/22/2025] [Accepted: 02/02/2025] [Indexed: 02/26/2025] Open
Abstract
Alzheimer's disease (AD) is a multifaceted neurodegenerative condition distinguished by the occurrence of memory impairment, cognitive deterioration, and neuronal impairment. Despite extensive research efforts, conventional treatment strategies primarily focus on symptom management, highlighting the need for innovative therapeutic approaches. This review explores the challenges of AD treatment and the integration of computational methodologies to advance therapeutic interventions. A comprehensive analysis of recent literature was conducted to elucidate the broad scope of Alzheimer's etiology and the limitations of conventional drug discovery approaches. Our findings underscore the critical role of computational models in elucidating disease mechanisms, identifying therapeutic targets, and expediting drug discovery. Through computational simulations, researchers can predict drug efficacy, optimize lead compounds, and facilitate personalized medicine approaches. Moreover, machine learning algorithms enhance early diagnosis and enable precision medicine strategies by analyzing multi-modal datasets. Case studies highlight the application of computational techniques in AD therapeutics, including the suppression of crucial proteins implicated in disease progression and the repurposing of existing drugs for AD management. Computational models elucidate the interplay between oxidative stress and neurodegeneration, offering insights into potential therapeutic interventions. Collaborative efforts between computational biologists, pharmacologists, and clinicians are essential to translate computational insights into clinically actionable interventions, ultimately improving patient outcomes and addressing the unmet medical needs of individuals affected by AD. Overall, integrating computational methodologies represents a promising paradigm shift in AD therapeutics, offering innovative solutions to overcome existing challenges and transform the landscape of AD treatment.
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Affiliation(s)
- Jibon Kumar Paul
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Abbeha Malik
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Pakistan
| | - Mahir Azmal
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tooba Gulzar
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Pakistan
| | - Muhammad Talal Rahim Afghan
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Pakistan
| | - Omar Faruk Talukder
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Samar Shahzadi
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Pakistan
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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3
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Bhutani K, Vishwakarma S, Yadav P, Yadav MK. The current landscape of aromatase inhibitors for the treatment of estrogen receptor-positive breast carcinoma. J Steroid Biochem Mol Biol 2025; 250:106729. [PMID: 40056742 DOI: 10.1016/j.jsbmb.2025.106729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 02/18/2025] [Accepted: 03/06/2025] [Indexed: 03/10/2025]
Abstract
Estrogen receptor-positive (ER+) breast carcinoma represents a significant portion of breast cancer cases and is characterized by the presence of estrogen receptors that promote tumor growth upon estrogen binding. ER + breast cancer progression involves hormonal influences, interactions within the tumor microenvironment, and genetic mutations that may lead to treatment resistance. Successful therapeutic options include hormonal therapies, particularly aromatase inhibitors (AIs), which aim to block the effects of estrogen or reduce its synthesis. With higher efficacy than tamoxifen, AIs such as anastrozole, letrozole, and exemestane have become widely employed in adjuvant and first-line treatments for advanced breast cancer. AIs function by inhibiting the enzyme aromatase, which converts androgens into estrogens in the peripheral tissues. Because too much estrogen might promote tumor growth, this decrease in estrogen levels is essential for treating ER+ malignancies. To provide a comprehensive overview of AIs in the treatment of ER+ breast cancer, this study examined the pharmacokinetics, clinical uses, mechanisms of action, and problems with treatment resistance. To maximize therapeutic approaches and enhance patient outcomes in the treatment of ER breast cancer, it is imperative to understand these characteristics.
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Affiliation(s)
- Khushboo Bhutani
- Department of Biotechnology, SRM University, Delhi-NCR, Sonepat, Haryana 131029, India
| | - Suyashi Vishwakarma
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh 201309, India
| | - Priyanka Yadav
- Department of Biotechnology, SRM University, Delhi-NCR, Sonepat, Haryana 131029, India
| | - Manoj Kumar Yadav
- Department of Biotechnology, SRM University, Delhi-NCR, Sonepat, Haryana 131029, India; Department of Biomedical Engineering, SRM University, Sonepat, Haryana 131029, India.
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4
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Miao X, Liu P, Liu Y, Zhang W, Li C, Wang X. Epigenetic targets and their inhibitors in the treatment of idiopathic pulmonary fibrosis. Eur J Med Chem 2025; 289:117463. [PMID: 40048798 DOI: 10.1016/j.ejmech.2025.117463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 02/24/2025] [Accepted: 02/26/2025] [Indexed: 03/29/2025]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a deadly lung disease characterized by fibroblast proliferation, excessive extracellular matrix buildup, inflammation, and tissue damage, resulting in respiratory failure and death. Recent studies suggest that impaired interactions among epithelial, mesenchymal, immune, and endothelial cells play a key role in IPF development. Advances in bioinformatics have also linked epigenetics, which bridges gene expression and environmental factors, to IPF. Despite the incomplete understanding of the pathogenic mechanisms underlying IPF, recent preclinical studies have identified several novel epigenetic therapeutic targets, including DNMT, EZH2, G9a/GLP, PRMT1/7, KDM6B, HDAC, CBP/p300, BRD4, METTL3, FTO, and ALKBH5, along with potential small-molecule inhibitors relevant for its treatment. This review explores the pathogenesis of IPF, emphasizing epigenetic therapeutic targets and potential small molecule drugs. It also analyzes the structure-activity relationships of these epigenetic drugs and summarizes their biological activities. The objective is to advance the development of innovative epigenetic therapies for IPF.
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Affiliation(s)
- Xiaohui Miao
- Department of Clinical Laboratory Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Pan Liu
- Department of Clinical Laboratory Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Yangyang Liu
- Department of Clinical Laboratory Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Wenying Zhang
- Department of Clinical Laboratory Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Chunxin Li
- Department of Clinical Laboratory Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Xiujiang Wang
- Department of Pulmonary Diseases, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130021, China.
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5
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Elalouf A, Elalouf H, Rosenfeld A, Maoz H. Artificial intelligence in drug resistance management. 3 Biotech 2025; 15:126. [PMID: 40235844 PMCID: PMC11996750 DOI: 10.1007/s13205-025-04282-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Accepted: 03/19/2025] [Indexed: 04/17/2025] Open
Abstract
This review highlights the application of artificial intelligence (AI), particularly deep learning and machine learning (ML), in managing antimicrobial resistance (AMR). Key findings demonstrate that AI models, such as Naïve Bayes, Decision Trees (DT), Random Forest (RF), Support Vector Machines (SVM), and Artificial Neural Networks (ANN), have significantly advanced the prediction of drug resistance patterns and the identification of novel antibiotics. These algorithms have effectively optimized antibiotic use, predicted resistance phenotypes, and identified new drug candidates. AI has also facilitated the detection of AMR-associated mutations, offering new insights into the spread of resistance and potential interventions. Despite data privacy and algorithm transparency challenges, AI presents a promising tool in combating AMR, with implications for improving patient outcomes, enhancing disease management, and addressing global public health concerns. However, realizing its full potential requires overcoming issues related to data scarcity, ethical considerations, and fostering interdisciplinary collaboration.
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Affiliation(s)
- Amir Elalouf
- Department of Management, Bar-Ilan University, 5290002 Ramat Gan, Israel
| | - Hadas Elalouf
- Department of Management, Bar-Ilan University, 5290002 Ramat Gan, Israel
| | - Ariel Rosenfeld
- Information Science Department, Bar-Ilan University, 5290002 Ramat Gan, Israel
| | - Hanan Maoz
- Department of Management, Bar-Ilan University, 5290002 Ramat Gan, Israel
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6
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Ding S, Alexander E, Liang H, Kulchar RJ, Singh R, Herzog RW, Daniell H, Leong KW. Synthetic and Biogenic Materials for Oral Delivery of Biologics: From Bench to Bedside. Chem Rev 2025; 125:4009-4068. [PMID: 40168474 DOI: 10.1021/acs.chemrev.4c00482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2025]
Abstract
The development of nucleic acid and protein drugs for oral delivery has lagged behind their production for conventional nonoral routes. Over the past decade, the evolution of DNA- and RNA-based technologies combined with the innovation of state-of-the-art delivery vehicles for nucleic acids has brought rapid advancements to the biopharmaceutical field. Nucleic acid therapies have the potential to achieve long-lasting effects, or even cures, by inhibiting or editing genes, which is not possible with conventional small-molecule drugs. However, challenges and limitations must be addressed before these therapies can provide cures for chronic conditions and rare diseases, rather than only offering temporary relief. Nucleic acids and proteins face premature degradation in the acidic, enzyme-rich stomach environment and are rapidly cleared by the liver. To overcome these challenges, various delivery vehicles have been developed to transport therapeutic compounds to the intestines, where the active compounds are released and gut microbiota and mucosal immune system also play an important role. This review provides a comprehensive overview of the promises and pitfalls associated with the oral route of administration of biologics, current delivery systems, applications of orally delivered therapeutics, and the challenges and considerations for translation of nucleic acid and protein therapeutics into clinical practice.
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Affiliation(s)
- Suwan Ding
- Department of Biomedical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Elena Alexander
- Department of Biomedical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Huiyi Liang
- Department of Biomedical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Rachel J Kulchar
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Philadelphia, Pennsylvania 19104, United States
| | - Rahul Singh
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Philadelphia, Pennsylvania 19104, United States
| | - Roland W Herzog
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Philadelphia, Pennsylvania 19104, United States
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
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Cai Y, Yang S, Zhao J, Zheng G, Han Y, Zhang Y, Qin Y, Yang C, Xiong Q, Chu X, Ju C, Yin H, Shi Y, Jiang F, Yong H, Zhu Y. Mechanism Exploration of Dietary Supplement Astaxanthin on Improving Atherosclerosis through an Integrated Strategy Encompassing Artificial Intelligence Virtual Screening and Experimental Validation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025. [PMID: 40265257 DOI: 10.1021/acs.jafc.4c11894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/24/2025]
Abstract
Atherosclerosis (AS) is a major and common pathological basis of ischemic intestinal infarction, myocardial infarction, stroke, renal failure, and other highly lethal and disabling diseases. Current pharmacological interventions (e.g., statins) often cause adverse effects, limiting their long-term use. Natural compounds, with their multitarget efficacy and superior safety profiles, have emerged as promising alternatives for AS treatment. As a potent antioxidant carotenoid, astaxanthin exhibits unique therapeutic potential by simultaneously targeting inflammation, oxidative stress, and lipid metabolism, which are key drivers of AS pathogenesis. This study will systematically decipher astaxanthin's therapeutic mechanisms through an integrative strategy encompassing artificial intelligence virtual screening and experimental validation. Notably, five proteins, including CTSD, DPP4, FABP5, ITGAL, and MMP9, were identified as core targets for astaxanthin intervention in AS via network pharmacology and machine learning. Meanwhile, the results from molecular dynamic simulations confirmed that these core targets can stable binding with astaxanthin. Furthermore, in vitro experiments further validated astaxanthin can inhibit foam cell formation, restore redox balance, and suppress inflammation. Moreover, a close correlation has been found between them. These findings position astaxanthin as a multitarget natural agent to combat AS, addressing both efficacy advantage and safety concerns of current therapies.
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Affiliation(s)
- Yisa Cai
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
- Translational Institute for Cancer Pain, Chongming Hospital Affiliated to Shanghai University of Health & Medicine Sciences (Xinhua Hospital Chongming Branch), Shanghai 202155, P. R. China
| | - Shiyan Yang
- Department of Internal Medicine, Huaian Hospital Affiliated to Xuzhou Medical University, Huai'an 223002, Jiangsu, P. R. China
| | - Jiajiang Zhao
- Yunnan Hongqingfu Biotechnology Co., LTD., Kunming 650000, Yunnan, P. R. China
| | - Guangzhen Zheng
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
| | - Yun Han
- School of Traditional Chinese Medicine, Binzhou Medical University, Yantai 264003, Shandong, P. R. China
| | - Yuhan Zhang
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
| | - Yiyuan Qin
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
| | - Chao Yang
- Translational Institute for Cancer Pain, Chongming Hospital Affiliated to Shanghai University of Health & Medicine Sciences (Xinhua Hospital Chongming Branch), Shanghai 202155, P. R. China
| | - Qingping Xiong
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
| | - Xinyi Chu
- Yunnan Hongqingfu Biotechnology Co., LTD., Kunming 650000, Yunnan, P. R. China
| | - Chunhan Ju
- Yunnan Hongqingfu Biotechnology Co., LTD., Kunming 650000, Yunnan, P. R. China
| | - Huixia Yin
- Yunnan Hongqingfu Biotechnology Co., LTD., Kunming 650000, Yunnan, P. R. China
| | - Yingying Shi
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
| | - Feng Jiang
- Translational Institute for Cancer Pain, Chongming Hospital Affiliated to Shanghai University of Health & Medicine Sciences (Xinhua Hospital Chongming Branch), Shanghai 202155, P. R. China
| | - Hui Yong
- Department of Cardiology, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huai'an 223000, Jiangsu, P. R. China
| | - Yong Zhu
- Jiangsu Key Laboratory of Regional Specific Resource Pharmaceutical Transformation, Huaiyin Institute of Technology, Huai'an 223003, Jiangsu, P. R. China
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8
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Gholap AD, Omri A. Advances in artificial intelligence-envisioned technologies for protein and nucleic acid research. Drug Discov Today 2025:104362. [PMID: 40252991 DOI: 10.1016/j.drudis.2025.104362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 02/04/2025] [Accepted: 04/10/2025] [Indexed: 04/21/2025]
Abstract
Artificial intelligence (AI) and machine learning (ML) have revolutionized pharmaceutical research, particularly in protein and nucleic acid studies. This review summarizes the current status of AI and ML applications in the pharmaceutical sector, focusing on innovative tools, web servers, and databases. This paper highlights how these technologies address key challenges in drug development including high costs, lengthy timelines, and the complexity of biological systems. Furthermore, the potential of AI in personalized medicine, cancer drug response prediction, and biomarker identification is discussed. The integration of AI and ML in pharmaceutical research promises to accelerate drug discovery, reduce development costs, and ultimately lead to more effective and personalized therapeutic strategies.
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Affiliation(s)
- Amol D Gholap
- Department of Pharmaceutics, St. John Institute of Pharmacy and Research, Palghar, Maharashtra 401404, India
| | - Abdelwahab Omri
- Department of Chemistry and Biochemistry, The Novel Drug and Vaccine Delivery Systems Facility, Laurentian University, Sudbury, ON P3E 2C6, Canada.
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Vajeethaveesin N, Kanitwithayanun J, Suriyo T, Chujan S, Satayavivad J. Perfluorooctane sulfonic acid: a possible risk factor of endothelial dysfunction based on in silico and in vitro studies. Arch Toxicol 2025:10.1007/s00204-025-04047-7. [PMID: 40244404 DOI: 10.1007/s00204-025-04047-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 03/27/2025] [Indexed: 04/18/2025]
Abstract
Perfluorooctane sulfonic acid (PFOS) is a fluorinated chemical utilized in a variety of industrial and household products. PFOS has been detected in human serum and is associated with multiple human adverse health effects. Epidemiological evidence has linked PFOS exposure to endothelial dysfunction, which is a key contributor to atherosclerosis. However, the underlying mechanisms of PFOS-induced endothelial dysfunction associated atherosclerosis has not been investigated. In the present study, human microvascular endothelial cells (HMEC-1) exposed to PFOS (15 μM) for 72 h, mimicking long-term exposure. We further employed integrated RNA-sequencing (RNA-seq) and transcriptomic analysis to identify differentially expressed genes (DEGs) for biological alterations: gene ontology (GO), pathway enrichment analysis (KEGG), protein-protein interaction network and modular clustering analysis. Furthermore, the Metascape database was used for disease association, tissue specificity, and transcription factor analysis. Hub genes were verified using atherosclerosis patient data sets from the GEO dataset. Alteration of hub genes in patients was then validated using immunoblotting and ELISA. Our results revealed that PFOS altered amino acid biosynthesis, lipid metabolism and induced the ER-stress response through the HRI/eIF2α/ATF4 pathway, leading to endothelial dysfunction. Interestingly, we found that PFOS induced inflammation by increasing COX-2, ICAM-1 and IL-6 expression through NF-κB and JAK2/STAT3 pathway in endothelial cells. Moreover, up-regulated C/EBPβ and ATF4 were observed in both patients and PFOS-exposed endothelium, which may use as an early biomarker and may have a potential role in PFOS-induced endothelial dysfunction. These findings provide novel insight into the underlying molecular mechanisms of PFOS-induced endothelial dysfunction associated with atherosclerosis.
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Affiliation(s)
- Nutsira Vajeethaveesin
- Environmental Toxicology Program, Chulabhorn Graduate Institute, Bangkok, 10210, Thailand
| | - Jantamas Kanitwithayanun
- Environmental Toxicology Program, Chulabhorn Graduate Institute, Bangkok, 10210, Thailand
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Center of Excellence On Environmental Health and Toxicology, Bangkok, 10400, Thailand
| | - Tawit Suriyo
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Center of Excellence On Environmental Health and Toxicology, Bangkok, 10400, Thailand
| | - Suthipong Chujan
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
- Center of Excellence On Environmental Health and Toxicology, Bangkok, 10400, Thailand.
| | - Jutamaad Satayavivad
- Environmental Toxicology Program, Chulabhorn Graduate Institute, Bangkok, 10210, Thailand.
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
- Center of Excellence On Environmental Health and Toxicology, Bangkok, 10400, Thailand.
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Woodring RN, Gurysh EG, Pulipaka T, Shilling KE, Stiepel RT, Pena ES, Bachelder EM, Ainslie KM. Supervised machine learning for predicting drug release from acetalated dextran nanofibers. Biomater Sci 2025. [PMID: 40237176 DOI: 10.1039/d5bm00259a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2025]
Abstract
Electrospun drug-loaded polymeric nanofibers can improve the efficacy of therapeutics for a variety of implications. By design, these biomaterial platforms can enhance drug bioavailability and site-specific delivery while reducing off-target toxicities when compared to other conventional formulations. By incorporating biocompatible and biodegradable polymers with tunable degradation rates, such as acetalated dextran (Ace-DEX), drug-loaded nanofibers can enhance the safety and efficacy of treatment regimens while improving patient compliance through controlled release. Despite these benefits, clinical translation of electrospun formulations is challenged by labor-intensive in vitro studies for ensuring that release kinetics are accurately characterized and reproducible. In this study, we report a novel workflow for assessing in vitro drug release from Ace-DEX nanofibers using machine learning (ML) and develop a predictive model to streamline this rate-limiting step. The developed Gaussian process regression (GPR) model was trained, validated, and optimized using in vitro release profiles from thirty electrospun Ace-DEX scaffolds. The results of GPR model simulations reveal consistent performance across all Ace-DEX formulations considered in this study while also demonstrating a drug-agnostic approach to predict fractional drug release over time.
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Affiliation(s)
- Ryan N Woodring
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
| | - Elizabeth G Gurysh
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
| | - Tanvi Pulipaka
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
| | - Kevin E Shilling
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
| | - Rebeca T Stiepel
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
| | - Erik S Pena
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, USA
| | - Eric M Bachelder
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
| | - Kristy M Ainslie
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at, Chapel Hill, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, USA
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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11
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Serra A, Fratello M, Federico A, Greco D. An update on knowledge graphs and their current and potential applications in drug discovery. Expert Opin Drug Discov 2025:1-21. [PMID: 40223439 DOI: 10.1080/17460441.2025.2490253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 04/03/2025] [Indexed: 04/15/2025]
Abstract
INTRODUCTION Knowledge graphs are becoming prominent tools in computational drug discovery. They effectively integrate heterogeneous biomedical data and generate new hypotheses and knowledge. AREAS COVERED This article is based on a literature review using Google Scholar and PubMed to retrieve articles on existing knowledge graphs relevant to the drug discovery field. The authors compare the types of entities, relationships, and data sources they encompass. Additionally, the authors provide examples of their use in the drug discovery field and discuss potential strategies for advancing this research area. EXPERT OPINION Knowledge graphs are crucial in drug discovery, but their construction leads to challenges in data integration and consistency. Future research should prioritize the standardization of data sources and data modeling. More efforts are needed for the integration in knowledge graphs of diverse data types, such as chemical structures and epigenetic data, to enhance their effectiveness. Additionally, advancements in large language models should be pursued to aid the development of knowledge graphs, provide intuitive querying capabilities for non-expert users, and explain knowledge graphs -derived predictions, thereby making these tools more accessible and their insights more interpretable for a wider audience.
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Affiliation(s)
- Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Antonio Federico
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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Aggarwal A, Bharadwaj S, Corredor G, Pathak T, Badve S, Madabhushi A. Artificial intelligence in digital pathology - time for a reality check. Nat Rev Clin Oncol 2025; 22:283-291. [PMID: 39934323 DOI: 10.1038/s41571-025-00991-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2025] [Indexed: 02/13/2025]
Abstract
The past decade has seen the introduction of artificial intelligence (AI)-based approaches aimed at optimizing several workflows across many medical specialties. In clinical oncology, the most promising applications include those involving image analysis, such as digital pathology. In this Perspective, we provide a comprehensive examination of the developments in AI in digital pathology between 2019 and 2024. We evaluate the current landscape from the lens of technological innovations, regulatory trends, deployment and implementation, reimbursement and commercial implications. We assess the technological advances that have driven improvements in AI, enabling more robust and scalable solutions for digital pathology. We also examine regulatory developments, in particular those affecting in-house devices and laboratory-developed tests, which are shaping the landscape of AI-based tools in digital pathology. Finally, we discuss the role of reimbursement frameworks and commercial investment in the clinical adoption of AI-based technologies. In this Perspective, we highlight both the progress and challenges in AI-driven digital pathology over the past 5 years, outlining the path forward for its adoption into routine practice in clinical oncology.
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Affiliation(s)
- Arpit Aggarwal
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Satvika Bharadwaj
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Germán Corredor
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Tilak Pathak
- Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
| | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Anant Madabhushi
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.
- Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA.
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13
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Golder S, Xu D, O'Connor K, Wang Y, Batra M, Hernandez GG. Leveraging Natural Language Processing and Machine Learning Methods for Adverse Drug Event Detection in Electronic Health/Medical Records: A Scoping Review. Drug Saf 2025; 48:321-337. [PMID: 39786481 PMCID: PMC11903561 DOI: 10.1007/s40264-024-01505-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2024] [Indexed: 01/12/2025]
Abstract
BACKGROUND Natural language processing (NLP) and machine learning (ML) techniques may help harness unstructured free-text electronic health record (EHR) data to detect adverse drug events (ADEs) and thus improve pharmacovigilance. However, evidence of their real-world effectiveness remains unclear. OBJECTIVE To summarise the evidence on the effectiveness of NLP/ML in detecting ADEs from unstructured EHR data and ultimately improve pharmacovigilance in comparison to other data sources. METHODS A scoping review was conducted by searching six databases in July 2023. Studies leveraging NLP/ML to identify ADEs from EHR were included. Titles/abstracts were screened by two independent researchers as were full-text articles. Data extraction was conducted by one researcher and checked by another. A narrative synthesis summarises the research techniques, ADEs analysed, model performance and pharmacovigilance impacts. RESULTS Seven studies met the inclusion criteria covering a wide range of ADEs and medications. The utilisation of rule-based NLP, statistical models, and deep learning approaches was observed. Natural language processing/ML techniques with unstructured data improved the detection of under-reported adverse events and safety signals. However, substantial variability was noted in the techniques and evaluation methods employed across the different studies and limitations exist in integrating the findings into practice. CONCLUSIONS Natural language processing (NLP) and machine learning (ML) have promising possibilities in extracting valuable insights with regard to pharmacovigilance from unstructured EHR data. These approaches have demonstrated proficiency in identifying specific adverse events and uncovering previously unknown safety signals that would not have been apparent through structured data alone. Nevertheless, challenges such as the absence of standardised methodologies and validation criteria obstruct the widespread adoption of NLP/ML for pharmacovigilance leveraging of unstructured EHR data.
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Affiliation(s)
- Su Golder
- Department of Health Sciences, University of York, York, YO10 5DD, UK.
| | - Dongfang Xu
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen O'Connor
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yunwen Wang
- William Allen White School of Journalism and Mass Communications, The University of Kansas, Lawrence, KS, USA
| | - Mahak Batra
- Department of Health Sciences, University of York, York, YO10 5DD, UK
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14
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Sutcliffe R, Doherty CPA, Morgan HP, Dunne NJ, McCarthy HO. Strategies for the design of biomimetic cell-penetrating peptides using AI-driven in silico tools for drug delivery. BIOMATERIALS ADVANCES 2025; 169:214153. [PMID: 39705787 DOI: 10.1016/j.bioadv.2024.214153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 12/08/2024] [Accepted: 12/14/2024] [Indexed: 12/23/2024]
Abstract
Cell-penetrating peptides (CPP) have gained rapid attention over the last 25 years; this is attributed to their versatility, customisation, and 'Trojan horse' delivery that evades the immune system. However, the current CPP rational design process is limited, as it requires several rounds of peptide synthesis, prediction and wet-lab validation, which is expensive, time-consuming and requires extensive knowledge in peptide chemistry. Artificial intelligence (AI) has emerged as a promising alternative which can augment the design process, for example by determining physiochemical characteristics, secondary structure, solvent accessibility, disorder and flexibility, as well as predicting in vivo behaviour such as toxicity and peptidase degradation. Other more recent tools utilise supervised machine learning (ML) to predict the penetrative ability of an amino acid sequence. The use of AI in the CPP design process has the potential to reduce development costs and increase the chances of success with respect to delivery. This review provides a survey of in silico tools and AI platforms which can be utilised in the design process, and the key features that should be taken into consideration when designing next generation CPPs.
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Affiliation(s)
- Rebecca Sutcliffe
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom of Great Britain and Northern Ireland
| | - Ciaran P A Doherty
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom of Great Britain and Northern Ireland; Antigenesis Biologics, Crossgar, Northern Ireland, United Kingdom of Great Britain and Northern Ireland
| | - Hugh P Morgan
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom of Great Britain and Northern Ireland; Antigenesis Biologics, Crossgar, Northern Ireland, United Kingdom of Great Britain and Northern Ireland
| | - Nicholas J Dunne
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom of Great Britain and Northern Ireland; School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin 9, Ireland
| | - Helen O McCarthy
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom of Great Britain and Northern Ireland.
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15
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Shirzad M, Salahvarzi A, Razzaq S, Javid-Naderi MJ, Rahdar A, Fathi-Karkan S, Ghadami A, Kharaba Z, Romanholo Ferreira LF. Revolutionizing prostate cancer therapy: Artificial intelligence - Based nanocarriers for precision diagnosis and treatment. Crit Rev Oncol Hematol 2025; 208:104653. [PMID: 39923922 DOI: 10.1016/j.critrevonc.2025.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 01/31/2025] [Accepted: 02/04/2025] [Indexed: 02/11/2025] Open
Abstract
Prostate cancer is one of the major health challenges in the world and needs novel therapeutic approaches to overcome the limitations of conventional treatment. This review delineates the transformative potential of artificial intelligence (AL) in enhancing nanocarrier-based drug delivery systems for prostate cancer therapy. With its ability to optimize nanocarrier design and predict drug delivery kinetics, AI has revolutionized personalized treatment planning in oncology. We discuss how AI can be integrated with nanotechnology to address challenges related to tumor heterogeneity, drug resistance, and systemic toxicity. Emphasis is placed on strong AI-driven advancements in the design of nanocarriers, structural optimization, targeting of ligands, and pharmacokinetics. We also give an overview of how AI can better predict toxicity, reduce costs, and enable personalized medicine. While challenges persist in the way of data accessibility, regulatory hurdles, and interactions with the immune system, future directions based on explainable AI (XAI) models, integration of multimodal data, and green nanocarrier designs promise to move the field forward. Convergence between AI and nanotechnology has been one key step toward safer, more effective, and patient-tailored cancer therapy.
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Affiliation(s)
- Maryam Shirzad
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Afsaneh Salahvarzi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sobia Razzaq
- School of Pharmacy, University of Management and Technology, Lahore SPH, Punjab, Pakistan
| | - Mohammad Javad Javid-Naderi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, Iran.
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd 94531-55166, Iran; Department of Medical Nanotechnology, School of Medicine, North Khorasan University of Medical Science, Bojnurd, Iran.
| | - Azam Ghadami
- Department of Chemical and Polymer Engineering, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Zelal Kharaba
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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16
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Gadhachanda KR, Marsool Marsool MD, Bozorgi A, Ameen D, Nayak SS, Nasrollahizadeh A, Alotaibi A, Farzaei A, Keivanlou MH, Hassanipour S, Amini-Salehi E, Jonnalagadda AK. Artificial intelligence in cardiovascular procedures: a bibliometric and visual analysis study. Ann Med Surg (Lond) 2025; 87:2187-2203. [PMID: 40212154 PMCID: PMC11981337 DOI: 10.1097/ms9.0000000000003112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 02/18/2025] [Indexed: 04/13/2025] Open
Abstract
Background The integration of artificial intelligence (AI) into cardiovascular procedures has significantly advanced diagnostic accuracy, outcome prediction, and robotic-assisted surgeries. However, a comprehensive bibliometric analysis of AI's impact in this field is lacking. This study examines research trends, key contributors, and emerging themes in AI-driven cardiovascular interventions. Methods We retrieved relevant publications from the Web of Science Core Collection and analyzed them using VOSviewer, CiteSpace, and Biblioshiny to map research trends and collaborations. Results AI-related cardiovascular research has grown substantially from 1993 to 2024, with a sharp increase from 2020 to 2023, peaking at 93 publications in 2023. The USA (127 papers), China (79), and England (31) were the top contributors, with Harvard University leading institutional output (17 papers). Frontiers in Cardiovascular Medicine was the most prolific journal. Core research themes included "machine learning," "mortality," and "cardiac surgery," with emerging trends in "association," "implantation," and "aortic stenosis," underscoring AI's expanding role in predictive modeling and surgical outcomes. Conclusion AI demonstrates transformative potential in cardiovascular procedures, particularly in diagnostic imaging, predictive modeling, and patient management. This bibliometric analysis highlights the growing interest in AI applications and provides a framework for integrating AI into clinical workflows to enhance diagnostic accuracy, treatment strategies, and patient outcomes.
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Affiliation(s)
| | | | - Ali Bozorgi
- Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Daniyal Ameen
- Department of Internal Medicine, Yale New Haven Health Bridgeport Hospital, Bridgeport, Connecticut, USA
| | - Sandeep Samethadka Nayak
- Department of Internal Medicine, Yale New Haven Health Bridgeport Hospital, Bridgeport, Connecticut, USA
| | | | | | - Alireza Farzaei
- Shahid Beheshti University of Medical Sciences, Tehran, Iran
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17
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Bobier C, Hurst DJ, Obeid J. Artificial intelligence, pharmaceutical development and dual-use research of concern: a call to action. JOURNAL OF MEDICAL ETHICS 2025:jme-2025-110750. [PMID: 40147882 DOI: 10.1136/jme-2025-110750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Accepted: 03/18/2025] [Indexed: 03/29/2025]
Abstract
Fervent attention was paid to what is coined dual-use research (DUR), or research that can both benefit and harm humanity, and dual-use research of concern (DURC), a particular subset of DUR that is reasonably anticipated to be a safety and security concern if misapplied. The aim of this paper is not to reiterate the challenges of DURC governance but to look at a new turn in DURC, namely the challenges posed by the use of artificial intelligence (AI) in pharmaceutical development. This is important, as AI is increasingly being used for pharmaceutical development in the industry. There is growing recognition that AI is DURC, and there is a dearth of industry and governmental guidance.
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Affiliation(s)
- Christopher Bobier
- Central Michigan University College of Medicine, Mount Pleasant, Michigan, USA
| | - Daniel J Hurst
- Director of Medical Professionalism, Ethics, & Humanities, Rowan-Virtua School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - John Obeid
- Central Michigan University College of Medicine, Mount Pleasant, Michigan, USA
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18
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Selvaraj C, Santhosh R, Alothaim AS, Vijayakumar R, Desai D, Safi SZ, Singh SK. Advances in cancer therapy: unveil the immunomodulatory protein involved in signaling pathways as molecular targets. CHEMICAL PAPERS 2025. [DOI: 10.1007/s11696-025-04007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 03/05/2025] [Indexed: 04/01/2025]
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19
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Bai Z, Osman M, Brendel M, Tangen CM, Flaig TW, Thompson IM, Plets M, Scott Lucia M, Theodorescu D, Gustafson D, Daneshmand S, Meeks JJ, Choi W, Dinney CPN, Elemento O, Lerner SP, McConkey DJ, Faltas BM, Wang F. Predicting response to neoadjuvant chemotherapy in muscle-invasive bladder cancer via interpretable multimodal deep learning. NPJ Digit Med 2025; 8:174. [PMID: 40121304 PMCID: PMC11929913 DOI: 10.1038/s41746-025-01560-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 03/11/2025] [Indexed: 03/25/2025] Open
Abstract
Building accurate prediction models and identifying predictive biomarkers for treatment response in Muscle-Invasive Bladder Cancer (MIBC) are essential for improving patient survival but remain challenging due to tumor heterogeneity, despite numerous related studies. To address this unmet need, we developed an interpretable Graph-based Multimodal Late Fusion (GMLF) deep learning framework. Integrating histopathology and cell type data from standard H&E images with gene expression profiles derived from RNA sequencing from the SWOG S1314-COXEN clinical trial (ClinicalTrials.gov NCT02177695 2014-06-25), GMLF uncovered new histopathological, cellular, and molecular determinants of response to neoadjuvant chemotherapy. Specifically, we identified key gene signatures that drive the predictive power of our model, including alterations in TP63, CCL5, and DCN. Our discovery can optimize treatment strategies for patients with MIBC, e.g., improving clinical outcomes, avoiding unnecessary treatment, and ultimately, bladder preservation. Additionally, our approach could be used to uncover predictors for other cancers.
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Affiliation(s)
- Zilong Bai
- Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Thomas W Flaig
- University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
| | - Ian M Thompson
- Children's Hospital of San Antonio, San Antonio, TX, USA
| | - Melissa Plets
- SWOG Statistics and Data Management Center, Seattle, WA, USA
| | - M Scott Lucia
- University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
| | | | - Daniel Gustafson
- University of Colorado Comprehensive Cancer Center, Aurora, CO, USA
| | - Siamak Daneshmand
- USC Institute of Urology, USC/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | - Fei Wang
- Weill Cornell Medicine, New York, NY, USA.
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20
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Mukherjee A, Sarkar R. Unlocking the microbial treasure trove: advances in Streptomyces derived secondary metabolites in the battle against cancer. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-04001-5. [PMID: 40100372 DOI: 10.1007/s00210-025-04001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Accepted: 02/27/2025] [Indexed: 03/20/2025]
Abstract
Streptomyces is widely recognized as the "biological factory" of specialized metabolites comprising a huge variety of bioactive molecules with diverse chemical properties. The potential of this Gram-positive soil bacteria to produce such diversified secondary metabolites with significant biological properties positions them as an ideal candidate for anticancer drug discovery. Some of the Streptomyces-derived secondary metabolites include siderophores (enterobactin, desferrioxamine), antibiotics (xiakemycin, dinactin) pigments (prodigiosin, melanin), and enzymes (L-methioninase, L-asperginase, cholesterol oxidase) which exhibit a pronounced anticancer effect on both in vitro and in vivo system. These secondary metabolites are endowed with antiproliferative, pro-apoptotic, antimetastatic, and antiangiogenic properties, presenting several promising characteristics that make them suitable candidates in the battle against this deadly disease. In this comprehensive review, we have dived deep and explored their history of discovery, their role as anticancer agents, underlying mechanisms, the approaches for the discovery of anticancer molecules from the secondary metabolites of Streptomyces (isolation of Streptomyces, characterization of bacterial strain, screening for anticancer activity and determination of in vitro and in vivo toxicity, structure-activity relationship studies, clinical translation, and drug development studies). The hurdles and challenges associated with this process and their future prospect were also illustrated. This review highlights the efficacy of Streptomyces as a "microbial treasure island" for novel anticancer agents, which warrants sustained research and exploration in this field to disclose more molecules from Streptomyces that are unidentified and to translate the clinical application of these secondary metabolites for cancer patients.
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Affiliation(s)
- Adrija Mukherjee
- B.D. Patel Institute of Paramedical Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388421, Gujarat, India
| | - Ruma Sarkar
- B.D. Patel Institute of Paramedical Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388421, Gujarat, India.
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21
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Esmaeilpour D, Ghomi M, Zare EN, Sillanpää M. Recent advances in DNA nanotechnology for cancer detection and therapy: A review. Int J Biol Macromol 2025; 307:142136. [PMID: 40107552 DOI: 10.1016/j.ijbiomac.2025.142136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 03/04/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025]
Abstract
Deoxyribonucleic acid (DNA) nanotechnology has rapidly emerged as a transformative field in biomedical research, offering innovative solutions for the detection and treatment of cancer. This review provides a comprehensive analysis of the role of DNA-based nanosystems in oncology, emphasizing their potential to address the limitations of conventional diagnostic and therapeutic approaches. Key advancements in DNA nanotechnology include the development of highly specific and sensitive nanostructures for early cancer detection, as well as precision-targeted delivery systems that enhance the efficacy of cancer therapies while minimizing side effects. The objectives of this review are threefold: first, to summarize the latest advancements in DNA nanotechnology, highlighting innovations in cancer biomarker detection and therapeutic applications; second, to explore the molecular mechanisms that enable these DNA-based nanosystems to interact with cancer cells with remarkable precision, including their design principles, self-assembly processes, and biological interactions; and third, to discuss the future implications of these technologies, considering the challenges, potential breakthroughs, and the steps needed to integrate DNA nanotechnology into clinical practice. By achieving these objectives, the review aims to offer insights into how DNA nanotechnology could revolutionize cancer care, providing new strategies for more personalized and effective treatments, and ultimately improving patient outcomes in the battle against cancer.
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Affiliation(s)
- Donya Esmaeilpour
- Center for Nanotechnology in Drug Delivery, School of Pharmacy, Shiraz University of Medical Science, Shiraz 71345-1583, Iran.
| | - Matineh Ghomi
- Department of Chemistry, Jundi-Shapur University of Technology, Dezful, Iran
| | - Ehsan Nazarzadeh Zare
- School of Chemistry, Damghan University, Damghan 36716-45667, Iran; Centre for Research Impact & Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India.
| | - Mika Sillanpää
- Institute of Research and Development, Duy Tan University, Da Nang, Viet Nam; School of Engineering & Technology, Duy Tan University, Da Nang, Viet Nam.
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El-Tanani M, Satyam SM, Rabbani SA, El-Tanani Y, Aljabali AAA, Al Faouri I, Rehman A. Revolutionizing Drug Delivery: The Impact of Advanced Materials Science and Technology on Precision Medicine. Pharmaceutics 2025; 17:375. [PMID: 40143038 PMCID: PMC11944361 DOI: 10.3390/pharmaceutics17030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 03/09/2025] [Accepted: 03/12/2025] [Indexed: 03/28/2025] Open
Abstract
Recent progress in material science has led to the development of new drug delivery systems that go beyond the conventional approaches and offer greater accuracy and convenience in the application of therapeutic agents. This review discusses the evolutionary role of nanocarriers, hydrogels, and bioresponsive polymers that offer enhanced drug release, target accuracy, and bioavailability. Oncology, chronic disease management, and vaccine delivery are some of the applications explored in this paper to show how these materials improve the therapeutic results, counteract multidrug resistance, and allow for sustained and localized treatments. The review also discusses the translational barriers of bringing advanced materials into the clinical setting, which include issues of biocompatibility, scalability, and regulatory approval. Methods to overcome these challenges include surface modifications to reduce immunogenicity, scalable production methods such as microfluidics, and the harmonization of regulatory systems. In addition, the convergence of artificial intelligence (AI) and machine learning (ML) is opening new frontiers in material science and personalized medicine. These technologies allow for predictive modeling and real-time adjustments to optimize drug delivery to the needs of individual patients. The use of advanced materials can also be applied to rare and underserved diseases; thus, new strategies in gene therapy, orphan drugs development, and global vaccine distribution may offer new hopes for millions of patients.
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Affiliation(s)
- Mohamed El-Tanani
- RAK College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
| | - Shakta Mani Satyam
- Department of Pharmacology, RAK College of Medical Sciences, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
| | - Syed Arman Rabbani
- RAK College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
| | | | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | - Ibrahim Al Faouri
- RAK College of Nursing, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
| | - Abdul Rehman
- Department of Pathology, RAK College of Medical Sciences, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates;
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Li X, Yue X, Zhang L, Zheng X, Shang N. Pharmacist-led surgical medicines prescription optimization and prediction service improves patient outcomes - a machine learning based study. Front Pharmacol 2025; 16:1534552. [PMID: 40160467 PMCID: PMC11949800 DOI: 10.3389/fphar.2025.1534552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 02/25/2025] [Indexed: 04/02/2025] Open
Abstract
Background Optimizing prescription practices for surgical patients is crucial due to the complexity and sensitivity of their medication regimens. To enhance medication safety and improve patient outcomes by introducing a machine learning (ML)-based warning model integrated into a pharmacist-led Surgical Medicines Prescription Optimization and Prediction (SMPOP) service. Method A retrospective cohort design with a prospective implementation phase was used in a tertiary hospital. The study was divided into three phases: (1) Data analysis and ML model development (1 April 2019 to 31 March 2022), (2) Establishment of a pharmacist-led management model (1 April 2022 to 31 March 2023), and (3) Outcome evaluation (1 April 2023 to 31 March 2024). Key variables, including gender, age, number of comorbidities, type of surgery, surgery complexity, days from hospitalization to surgery, type of prescription, type of medication, route of administration, and prescriber's seniority were collected. The data set was divided into training set and test set in the form of 8:2. The effectiveness of the SMPOP service was evaluated based on prescription appropriateness, adverse drug reactions (ADRs), length of hospital stay, total hospitalization costs, and medication expenses. Results In Phase 1, 6,983 prescriptions were identified as potential prescription errors (PPEs) for ML model development, with 43.9% of them accepted by prescribers. The Random Forest (RF) model performed the best (AUC = 0.893) and retained high accuracy with 12 features (AUC = 0.886). External validation showed an AUC of 0.786. In Phase 2, SMPOP services were implemented, which effectively promoted effective communication between pharmacists and physicians and ensured the successful implementation of intervention measures. The SMPOP service was fully implemented. In Phase 3, the acceptance rate of pharmacist recommendations rose to 71.3%, while the length of stay, total hospitalization costs, and medication costs significantly decreased (p < 0.05), indicating overall improvement compared to Phase 1. Conclusion SMPOP service enhances prescription appropriateness, reduces ADRs, shortens stays, and lowers costs, underscoring the need for continuous innovation in healthcare.
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Affiliation(s)
- Xianlin Li
- Department of Pharmacy, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiunan Yue
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Lan Zhang
- School of Public Health, Capital Medical University, Beijing, China
| | - Xiaojun Zheng
- Department of Pharmacy, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Nan Shang
- Department of Pharmacy, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
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24
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Noury H, Rahdar A, Romanholo Ferreira LF, Jamalpoor Z. AI-driven innovations in smart multifunctional nanocarriers for drug and gene delivery: A mini-review. Crit Rev Oncol Hematol 2025; 210:104701. [PMID: 40086770 DOI: 10.1016/j.critrevonc.2025.104701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Revised: 03/07/2025] [Accepted: 03/07/2025] [Indexed: 03/16/2025] Open
Abstract
The convergence of artificial intelligence (AI) and nanomedicine has revolutionized the design of smart multifunctional nanocarriers (SMNs) for drug and gene delivery, offering unprecedented precision, efficiency, and personalization in therapeutic applications. AI-driven approaches enhance the development of these nanocarriers by accelerating their design, optimizing drug loading and release kinetics, improving biocompatibility, and predicting interactions with biological barriers. This review explores the transformative role of AI in the fabrication and functionalization of SMNs, emphasizing its impact on overcoming challenges in targeted drug delivery, controlled release, and theranostics. We discuss the integration of AI with advanced nanomaterials-such as polymeric, lipidic, and inorganic nanoparticles-highlighting their potential in oncology and hematology. Furthermore, we examine recent clinical and preclinical case studies demonstrating AI-assisted nanocarrier development for personalized medicine. The synergy between AI and nanotechnology paves the way for next-generation precision therapeutics, addressing critical limitations in traditional drug delivery systems. However, data standardization, regulatory compliance, and translational scalability challenges remain. This review underscores the need for interdisciplinary collaboration to unlock AI's potential in nanomedicine fully, ultimately advancing the clinical application of SMNs for more effective and safer patient care.
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Affiliation(s)
- Hamid Noury
- Health Research Center, Chamran Hospital, Tehran, Iran
| | - Abbas Rahdar
- Department of Physics, Faculty of Sciences, University of Zabol, Zabol 538-98615, Iran.
| | | | - Zahra Jamalpoor
- Trauma and Surgery Research Center, Aja University of Medical Sciences, Tehran, Iran.
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25
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Roy B, Cao K, Singh CO, Fang X, Yang H, Wei D. Advances in gut microbiota-related treatment strategies for managing colorectal cancer in humans. Cancer Biol Med 2025; 22:j.issn.2095-3941.2024.0263. [PMID: 40072039 PMCID: PMC11899591 DOI: 10.20892/j.issn.2095-3941.2024.0263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 01/15/2025] [Indexed: 03/15/2025] Open
Abstract
Colorectal cancer (CRC) is a major contributor to global cancer-related mortality with increasing incidence rates in both developed and developing regions. Therefore, CRC presents a significant challenge to global health. The development of innovative tools for enhancing early CRC screening and diagnosis, along with novel treatments and therapies for improved management, remains an urgent necessity. CRC is intricately associated with the gut microbiota, which is integral to food digestion, nutrient generation, drug metabolism, metabolite production, immune enhancement, endocrine regulation, neurogenesis modulation, and the maintenance of physiologic and psychological equilibrium. Dysbiosis or imbalances in the gut microbiome have been implicated in various disorders, including CRC. Emerging evidence highlights the critical role of the gut microbiome in CRC pathogenesis and treatment, which presents potential opportunities for early detection and diagnosis. Despite substantial advances in understanding the relationship between the gut microbiota and CRC, significant challenges persist. Gaining a deeper and more detailed understanding of the interactions between the human microbiota and cancer is essential to fully realize the potential of the microbiota in cancer management. Unlike genetic factors, the gut microbiome is subject to modification, offering a promising avenue for the development of CRC treatments and drug discovery. This review provides an overview of the interactions between the human gut microbiome and CRC, while examining prospects for precision management of CRC.
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Affiliation(s)
- Bhaskar Roy
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Science, Hangzhou 310022, China
| | - Kunfeng Cao
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Science, Hangzhou 310022, China
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | | | - Huanming Yang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Science, Hangzhou 310022, China
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310029, China
| | - Dong Wei
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Science, Hangzhou 310022, China
- BGI Research, Shenzhen 518083, China
- Clin Lab, BGI Genomics, Beijing 100000, China
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26
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Youssef E, Palmer D, Fletcher B, Vaughn R. Exosomes in Precision Oncology and Beyond: From Bench to Bedside in Diagnostics and Therapeutics. Cancers (Basel) 2025; 17:940. [PMID: 40149276 PMCID: PMC11940788 DOI: 10.3390/cancers17060940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 02/28/2025] [Accepted: 03/07/2025] [Indexed: 03/29/2025] Open
Abstract
Exosomes have emerged as pivotal players in precision oncology, offering innovative solutions to longstanding challenges such as metastasis, therapeutic resistance, and immune evasion. These nanoscale extracellular vesicles facilitate intercellular communication by transferring bioactive molecules that mirror the biological state of their parent cells, positioning them as transformative tools for cancer diagnostics and therapeutics. Recent advancements in exosome engineering, artificial intelligence (AI)-driven analytics, and isolation technologies are breaking barriers in scalability, reproducibility, and clinical application. Bioengineered exosomes are being leveraged for CRISPR-Cas9 delivery, while AI models are enhancing biomarker discovery and liquid biopsy accuracy. Despite these advancements, key obstacles such as heterogeneity in exosome populations and the lack of standardized isolation protocols persist. This review synthesizes pioneering research on exosome biology, molecular engineering, and clinical translation, emphasizing their dual roles as both mediators of tumor progression and tools for intervention. It also explores emerging areas, including microbiome-exosome interactions and the integration of machine learning in exosome-based precision medicine. By bridging innovation with translational strategies, this work charts a forward-looking path for integrating exosomes into next-generation cancer care, setting it apart as a comprehensive guide to overcoming clinical and technological hurdles in this rapidly evolving field.
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Gangwal A, Lavecchia A. AI-Driven Drug Discovery for Rare Diseases. J Chem Inf Model 2025; 65:2214-2231. [PMID: 39689164 DOI: 10.1021/acs.jcim.4c01966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2024]
Abstract
Rare diseases (RDs), affecting 300 million people globally, present a daunting public health challenge characterized by complexity, limited treatment options, and diagnostic hurdles. Despite legislative efforts, such as the 1983 US Orphan Drug Act, more than 90% of RDs lack effective therapies. Traditional drug discovery models, marked by lengthy development cycles and high failure rates, struggle to meet the unique demands of RDs, often yielding poor returns on investment. However, the advent of artificial intelligence (AI), encompassing machine learning (ML) and deep learning (DL), offers groundbreaking solutions. This review explores AI's potential to revolutionize drug discovery for RDs by overcoming these challenges. It discusses AI-driven advancements, such as drug repurposing, biomarker discovery, personalized medicine, genetics, clinical trial optimization, corporate innovations, and novel drug target identification. By synthesizing current knowledge and recent breakthroughs, this review provides crucial insights into how AI can accelerate therapeutic development for RDs, ultimately improving patient outcomes. This comprehensive analysis fills a critical gap in the literature, enhancing understanding of AI's pivotal role in transforming RD research and guiding future research and development efforts in this vital area of medicine.
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Affiliation(s)
- Amit Gangwal
- Department of Natural Product Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule 424001, Maharashtra, India
| | - Antonio Lavecchia
- "Drug Discovery" Laboratory, Department of Pharmacy, University of Naples Federico II, I-80131 Naples, Italy
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Šoša I, Perković M, Baniček Šoša I, Grubešić P, Linšak DT, Strenja I. Absorption of Toxicants from the Ocular Surface: Potential Applications in Toxicology. Biomedicines 2025; 13:645. [PMID: 40149621 PMCID: PMC11940235 DOI: 10.3390/biomedicines13030645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 02/17/2025] [Accepted: 03/04/2025] [Indexed: 03/29/2025] Open
Abstract
In relation to the eye, the body can absorb substances from the ocular surface fluid (OSF) in a few ways: directly through the conjunctival sac, through the nasal mucosa as the fluid drains into the nose, or through ingestion. Regardless of the absorption method, fluid from the conjunctival sac should be used as a toxicological matrix, even though only small quantities are needed. Contemporary analytical techniques make it a suitable matrix for toxicological research. Analyzing small quantities of the matrix and nano-quantities of the analyte requires high-cost, sophisticated tools, which is particularly relevant in the high-throughput environment of new drug or cosmetics testing. Environmental toxicology also presents a challenge, as many pollutants can enter the system using the same ocular surface route. A review of the existing literature was conducted to assess potential applications in clinical and forensic toxicology related to the absorption of toxicants from the ocular surface. The selection of the studies used in this review aimed to identify new, more efficient, and cost-effective analytical technology and diagnostic methods.
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Affiliation(s)
- Ivan Šoša
- Department of Anatomy, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Manuela Perković
- Department of Pathology and Cytology, Pula General Hospital, 52100 Pula, Croatia;
| | - Ivanka Baniček Šoša
- Clinical Hospital Centre Rijeka, University Department of Physical and Rehabilitation Medicine, Krešimirova 42, 51000 Rijeka, Croatia;
| | - Petra Grubešić
- Department of Ophthalmology, Clinical Hospital Center Rijeka, Krešmirova 42, 51000 Rijeka, Croatia;
| | - Dijana Tomić Linšak
- Department for Health Ecology, Faculty of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia;
- Department for Scientific and Teaching Activity, Teaching Institute of Public Health County of Primorje-Gorski Kotar, Krešimirova 52a, 51000 Rijeka, Croatia
| | - Ines Strenja
- Department of Neurology University Hospital Centre Rijeka, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia;
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Sadanov AK, Baimakhanova BB, Orasymbet SE, Ratnikova IA, Turlybaeva ZZ, Baimakhanova GB, Amitova AA, Omirbekova AA, Aitkaliyeva GS, Kossalbayev BD, Belkozhayev AM. Engineering Useful Microbial Species for Pharmaceutical Applications. Microorganisms 2025; 13:599. [PMID: 40142492 PMCID: PMC11944651 DOI: 10.3390/microorganisms13030599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Revised: 03/01/2025] [Accepted: 03/03/2025] [Indexed: 03/28/2025] Open
Abstract
Microbial engineering has made a significant breakthrough in pharmaceutical biotechnology, greatly expanding the production of biologically active compounds, therapeutic proteins, and novel drug candidates. Recent advancements in genetic engineering, synthetic biology, and adaptive evolution have contributed to the optimization of microbial strains for pharmaceutical applications, playing a crucial role in enhancing their productivity and stability. The CRISPR-Cas system is widely utilized as a precise genome modification tool, enabling the enhancement of metabolite biosynthesis and the activation of synthetic biological pathways. Additionally, synthetic biology approaches allow for the targeted design of microorganisms with improved metabolic efficiency and therapeutic potential, thereby accelerating the development of new pharmaceutical products. The integration of artificial intelligence (AI) and machine learning (ML) plays a vital role in further advancing microbial engineering by predicting metabolic network interactions, optimizing bioprocesses, and accelerating the drug discovery process. However, challenges such as the efficient optimization of metabolic pathways, ensuring sustainable industrial-scale production, and meeting international regulatory requirements remain critical barriers in the field. Furthermore, to mitigate potential risks, it is essential to develop stringent biocontainment strategies and implement appropriate regulatory oversight. This review comprehensively examines recent innovations in microbial engineering, analyzing key technological advancements, regulatory challenges, and future development perspectives.
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Affiliation(s)
- Amankeldi K. Sadanov
- LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan; (A.K.S.); (B.B.B.); (S.E.O.); (I.A.R.); (Z.Z.T.)
| | - Baiken B. Baimakhanova
- LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan; (A.K.S.); (B.B.B.); (S.E.O.); (I.A.R.); (Z.Z.T.)
| | - Saltanat E. Orasymbet
- LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan; (A.K.S.); (B.B.B.); (S.E.O.); (I.A.R.); (Z.Z.T.)
| | - Irina A. Ratnikova
- LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan; (A.K.S.); (B.B.B.); (S.E.O.); (I.A.R.); (Z.Z.T.)
| | - Zere Z. Turlybaeva
- LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan; (A.K.S.); (B.B.B.); (S.E.O.); (I.A.R.); (Z.Z.T.)
| | - Gul B. Baimakhanova
- LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan; (A.K.S.); (B.B.B.); (S.E.O.); (I.A.R.); (Z.Z.T.)
| | - Aigul A. Amitova
- Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan; (G.S.A.); (A.M.B.)
| | - Anel A. Omirbekova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan;
| | - Gulzat S. Aitkaliyeva
- Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan; (G.S.A.); (A.M.B.)
| | - Bekzhan D. Kossalbayev
- Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan; (G.S.A.); (A.M.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan;
- Ecology Research Institute, Khoja Akhmet Yassawi International Kazakh-Turkish University, Turkistan 161200, Kazakhstan
| | - Ayaz M. Belkozhayev
- Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan; (G.S.A.); (A.M.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan;
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30
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Zhu Z, Wang Y, Qi Z, Hu W, Zhang X, Wagner SK, Wang Y, Ran AR, Ong J, Waisberg E, Masalkhi M, Suh A, Tham YC, Cheung CY, Yang X, Yu H, Ge Z, Wang W, Sheng B, Liu Y, Lee AG, Denniston AK, Wijngaarden PV, Keane PA, Cheng CY, He M, Wong TY. Oculomics: Current concepts and evidence. Prog Retin Eye Res 2025; 106:101350. [PMID: 40049544 DOI: 10.1016/j.preteyeres.2025.101350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 03/03/2025] [Accepted: 03/03/2025] [Indexed: 03/20/2025]
Abstract
The eye provides novel insights into general health, as well as pathogenesis and development of systemic diseases. In the past decade, growing evidence has demonstrated that the eye's structure and function mirror multiple systemic health conditions, especially in cardiovascular diseases, neurodegenerative disorders, and kidney impairments. This has given rise to the field of oculomics-the application of ophthalmic biomarkers to understand mechanisms, detect and predict disease. The development of this field has been accelerated by three major advances: 1) the availability and widespread clinical adoption of high-resolution and non-invasive ophthalmic imaging ("hardware"); 2) the availability of large studies to interrogate associations ("big data"); 3) the development of novel analytical methods, including artificial intelligence (AI) ("software"). Oculomics offers an opportunity to enhance our understanding of the interplay between the eye and the body, while supporting development of innovative diagnostic, prognostic, and therapeutic tools. These advances have been further accelerated by developments in AI, coupled with large-scale linkage datasets linking ocular imaging data with systemic health data. Oculomics also enables the detection, screening, diagnosis, and monitoring of many systemic health conditions. Furthermore, oculomics with AI allows prediction of the risk of systemic diseases, enabling risk stratification, opening up new avenues for prevention or individualized risk prediction and prevention, facilitating personalized medicine. In this review, we summarise current concepts and evidence in the field of oculomics, highlighting the progress that has been made, remaining challenges, and the opportunities for future research.
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Affiliation(s)
- Zhuoting Zhu
- Centre for Eye Research Australia, Ophthalmology, University of Melbourne, Melbourne, VIC, Australia; Department of Surgery (Ophthalmology), University of Melbourne, Melbourne, VIC, Australia.
| | - Yueye Wang
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ziyi Qi
- Centre for Eye Research Australia, Ophthalmology, University of Melbourne, Melbourne, VIC, Australia; Department of Surgery (Ophthalmology), University of Melbourne, Melbourne, VIC, Australia; Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Eye Diseases, Shanghai, China
| | - Wenyi Hu
- Centre for Eye Research Australia, Ophthalmology, University of Melbourne, Melbourne, VIC, Australia; Department of Surgery (Ophthalmology), University of Melbourne, Melbourne, VIC, Australia
| | - Xiayin Zhang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Siegfried K Wagner
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Ophthalmology, University College London, London, UK
| | - Yujie Wang
- Centre for Eye Research Australia, Ophthalmology, University of Melbourne, Melbourne, VIC, Australia; Department of Surgery (Ophthalmology), University of Melbourne, Melbourne, VIC, Australia
| | - An Ran Ran
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Joshua Ong
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, Ann Arbor, USA
| | - Ethan Waisberg
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mouayad Masalkhi
- University College Dublin School of Medicine, Belfield, Dublin, Ireland
| | - Alex Suh
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Yih Chung Tham
- Department of Ophthalmology and Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore
| | - Carol Y Cheung
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong Yang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Honghua Yu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zongyuan Ge
- Monash e-Research Center, Faculty of Engineering, Airdoc Research, Nvidia AI Technology Research Center, Monash University, Melbourne, VIC, Australia
| | - Wei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bin Sheng
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Liu
- Google Research, Mountain View, CA, USA
| | - Andrew G Lee
- Center for Space Medicine and the Department of Ophthalmology, Baylor College of Medicine, Houston, USA; Department of Ophthalmology, Blanton Eye Institute, Houston Methodist Hospital, Houston, USA; The Houston Methodist Research Institute, Houston Methodist Hospital, Houston, USA; Departments of Ophthalmology, Neurology, and Neurosurgery, Weill Cornell Medicine, New York, USA; Department of Ophthalmology, University of Texas Medical Branch, Galveston, USA; University of Texas MD Anderson Cancer Center, Houston, USA; Texas A&M College of Medicine, Bryan, USA; Department of Ophthalmology, The University of Iowa Hospitals and Clinics, Iowa City, USA
| | - Alastair K Denniston
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Ophthalmology, University College London, London, UK; National Institute for Health and Care Research (NIHR) Birmingham Biomedical Research Centre (BRC), University Hospital Birmingham and University of Birmingham, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Birmingham Health Partners Centre for Regulatory Science and Innovation, University of Birmingham, Birmingham, UK
| | - Peter van Wijngaarden
- Centre for Eye Research Australia, Ophthalmology, University of Melbourne, Melbourne, VIC, Australia; Department of Surgery (Ophthalmology), University of Melbourne, Melbourne, VIC, Australia; Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Pearse A Keane
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Ophthalmology, University College London, London, UK
| | - Ching-Yu Cheng
- Department of Ophthalmology and Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore
| | - Mingguang He
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore; School of Clinical Medicine, Beijing Tsinghua Changgung Hospital, Tsinghua Medicine, Tsinghua University, Beijing, China.
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Khan Y, Rizvi S, Raza A, Khan A, Hussain S, Khan NU, Alshammari SO, Alshammari QA, Alshammari A, Ellakwa DES. Tailored therapies for triple-negative breast cancer: current landscape and future perceptions. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-03896-4. [PMID: 40029385 DOI: 10.1007/s00210-025-03896-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 02/07/2025] [Indexed: 03/05/2025]
Abstract
Triple-negative breast cancer (TNBC) has become one of the most challenging cancers to date due to its great variability in biological features, high growth rate, and rare options for treatment. This review examines several innovative strategies for tailored treatment of TNBC, focusing mainly on the most recent developments and potential directions. The molecular landscape of TNBC is covered in the first section, which keeps the focus on transcriptome and genomic profiling while highlighting key molecular targets like mutations in the BRCA1/2, PIK3CA, androgen receptors (AR), epidermal growth factor receptors (EGFR), and immunological checkpoint molecules. This review also covers novel therapies that aim to block well-defined pathways, including immune checkpoint inhibitors (ICI), EGFR inhibitors, drugs that target AR, poly ADP ribose polymerase (PARP) inhibitors, and drugs that disrupt the PI3K/AKT/mTOR pathway. Additionally, it covers novel strategies focusing on combination therapy, targeting the DNA damage response pathway, and epigenetic modulators. Conclusively, it emphasizes perspectives and directions on topics such as personalized medicine, artificial intelligence (AI), predictive biomarkers, and treatment planning with the inclusion of machine learning (ML).
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Affiliation(s)
- Yumna Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, 25130, Pakistan.
| | - Sana Rizvi
- Bakhtawar Amin Medical and Dental College, Bakhtawar Amin Trust Teaching Hospital, Multan, Pakistan
| | - Ali Raza
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Amna Khan
- Abbottabad International Medical Institute, Abbottabad, 22020, Pakistan
| | - Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand, 248007, India
| | - Najeeb Ullah Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, 25130, Pakistan
| | - Saud O Alshammari
- Department of Pharmacognosy and Alternative Medicine, College of Pharmacy, Northern Border University, 76321, Rafha, Saudi Arabia
| | - Qamar A Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, Northern Border University, Rafha, Saudi Arabia
| | - Abdulkarim Alshammari
- Department of Clinical Practice, College of Pharmacy, Northern Border University, Rafha, Saudi Arabia
| | - Doha El-Sayed Ellakwa
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy for Girls, Al-Azhar University, Cairo, Egypt.
- Department of Biochemistry, Faculty of Pharmacy, Sinai University, Kantra Branch, Ismailia, Egypt.
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32
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Vaghasiya J, Khan M, Milan Bakhda T. A meta-analysis of AI and machine learning in project management: Optimizing vaccine development for emerging viral threats in biotechnology. Int J Med Inform 2025; 195:105768. [PMID: 39708670 DOI: 10.1016/j.ijmedinf.2024.105768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 12/12/2024] [Accepted: 12/16/2024] [Indexed: 12/23/2024]
Abstract
OBJECTIVES Artificial Intelligence (AI) and Machine Learning (ML) have emerged as transformative technologies across various industries, including healthcare, biotechnology, and vaccine development. These technologies offer immense potential to improve project management efficiency, decision-making, and resource utilization, especially in complex tasks such as vaccine development and healthcare innovations. METHODS A systematic meta-analysis was conducted by reviewing studies from databases like PubMed, IEEE Xplore, Scopus, Web of Science, EMBASE, and Google Scholar until September 2024. The analysis focused on the application of AI and ML in project management for vaccine development, biotechnology, and broader healthcare innovations using the PICO framework to guide study selection and inclusion. Statistical analyses were performed using Review Manager 5.4 and Comprehensive Meta-Analysis (CMA) software. RESULTS The meta-analysis reviewed 44 studies examining the integration of Artificial Intelligence (AI) and Machine Learning (ML) in healthcare, biotechnology, and vaccine development project management. Results demonstrated significant improvements in efficiency, resource allocation, decision-making, and risk management. AI/ML applications notably accelerated vaccine development, from candidate identification to clinical trial optimization, and improved predictive modeling for efficacy and safety. Subgroup analysis revealed variations in effectiveness across healthcare sectors, with the highest pooled effect sizes observed in infectious disease control (1.2; 95 % CI: 0.85-1.50) compared to medical imaging (0.85; 95 % CI: 0.75-0.95). Studies employing AI techniques demonstrated a pooled effect size of 0.83 (95 % CI: 0.78-1.08). Despite the observed high heterogeneity (I2 = 99.04 %) and moderate-to-high risks of bias, sensitivity analyses confirmed the robustness of the findings. Overall, AI/ML integration offers transformative potential to enhance project management and vaccine development, driving innovation and efficiency in these critical fields. CONCLUSION AI and ML technologies show significant potential to transform project management practices in healthcare, biotechnology, and vaccine development by enhancing efficiency, predictive analytics, and decision-making capabilities. Their integration paves the way for more innovative, data-driven solutions that can adapt to evolving challenges in these fields.
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Affiliation(s)
- Jatin Vaghasiya
- Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States
| | - Mahim Khan
- Health Biotechnology Division, Pakistan Institute of Engineering and Applied Sciences, National Institute for Biotechnology and Genetic Engineering College, (NIBGE-C, PIEAS), Faisalabad, Punjab 38000, Pakistan.
| | - Tarak Milan Bakhda
- Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States.
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Foote HP, Hong C, Anwar M, Borentain M, Bugin K, Dreyer N, Fessel J, Goyal N, Hanger M, Hernandez AF, Hornik CP, Jackman JG, Lindsay AC, Matheny ME, Ozer K, Seidel J, Stockbridge N, Embi PJ, Lindsell CJ. Embracing Generative Artificial Intelligence in Clinical Research and Beyond: Opportunities, Challenges, and Solutions. JACC. ADVANCES 2025; 4:101593. [PMID: 39923329 PMCID: PMC11850149 DOI: 10.1016/j.jacadv.2025.101593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 12/30/2024] [Accepted: 01/03/2025] [Indexed: 02/11/2025]
Abstract
To explore threats and opportunities and to chart a path for safely navigating the rapid changes that generative artificial intelligence (AI) will bring to clinical research, the Duke Clinical Research Institute convened a multidisciplinary think tank in January 2024. Leading experts from academia, industry, nonprofits, and government agencies highlighted the potential opportunities of generative AI in automation of documentation, strengthening of participant and community engagement, and improvement of trial accuracy and efficiency. Challenges include technical hurdles, ethical dilemmas, and regulatory uncertainties. Success is expected to require establishing rigorous data management and security protocols, fostering integrity and trust among stakeholders, and sharing information about the safety and effectiveness of AI applications. Meeting insights point towards a future where, through collaboration and transparency, generative AI will help to shorten the translational pipeline and increase the inclusivity and equitability of clinical research.
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Affiliation(s)
- Henry P Foote
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA; Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Mohd Anwar
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Kevin Bugin
- United States Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Josh Fessel
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Morgan Hanger
- Clinical Trials Transformation Initiative Duke Clinical Research Institute, North Carolina, USA
| | | | | | | | | | | | - Kerem Ozer
- Novo Nordisk, Plainsboro, New Jersey, USA
| | - Jan Seidel
- Boehringer Ingelheim, Plainsboro, New Jersey, USA
| | - Norman Stockbridge
- United States Food and Drug Administration, Silver Spring, Maryland, USA
| | - Peter J Embi
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Xia M, Wang J, Huang F. Exploring the impact and implications of artificial intelligence in the field of nursing. J Clin Nurs 2025; 34:1096-1098. [PMID: 38822494 DOI: 10.1111/jocn.17312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Affiliation(s)
- Mengjie Xia
- School of Medicine, Taizhou University, Jiaojiang, Zhejiang, China
- School of Nursing, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Selangor, Malaysia
| | - Junqiang Wang
- Department of Obstetrics and Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao, Zhejiang, China
| | - Fang Huang
- School of Medicine, Taizhou University, Jiaojiang, Zhejiang, China
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Moni SS, Moshi JM, Matou-Nasri S, Alotaibi S, Hawsawi YM, Elmobark ME, Hakami AMS, Jeraiby MA, Sulayli AA, Moafa HN. Advances in Materials Science for Precision Melanoma Therapy: Nanotechnology-Enhanced Drug Delivery Systems. Pharmaceutics 2025; 17:296. [PMID: 40142960 PMCID: PMC11945159 DOI: 10.3390/pharmaceutics17030296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 02/14/2025] [Accepted: 02/19/2025] [Indexed: 03/28/2025] Open
Abstract
Melanoma, a highly aggressive form of skin cancer, poses a major therapeutic challenge due to its metastatic potential, resistance to conventional therapies, and the complexity of the tumor microenvironment (TME). Materials science and nanotechnology advances have led to using nanocarriers such as liposomes, dendrimers, polymeric nanoparticles, and metallic nanoparticles as transformative solutions for precision melanoma therapy. This review summarizes findings from Web of Science, PubMed, EMBASE, Scopus, and Google Scholar and highlights the role of nanotechnology in overcoming melanoma treatment barriers. Nanoparticles facilitate passive and active targeting through mechanisms such as the enhanced permeability and retention (EPR) effect and functionalization with tumor-specific ligands, thereby improving the accuracy of drug delivery and reducing systemic toxicity. Stimuli-responsive systems and multi-stage targeting further improve therapeutic precision and overcome challenges such as poor tumor penetration and drug resistance. Emerging therapeutic platforms combine diagnostic imaging with therapeutic delivery, paving the way for personalized medicine. However, there are still issues with scalability, biocompatibility, and regulatory compliance. This comprehensive review highlights the potential of integrating nanotechnology with advances in genetics and proteomics, scalable, and patient-specific therapies. These interdisciplinary innovations promise to redefine the treatment of melanoma and provide safer, more effective, and more accessible treatments. Continued research is essential to bridge the gap between evidence-based scientific advances and clinical applications.
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Affiliation(s)
- Sivakumar S. Moni
- College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia;
- Health Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Jobran M. Moshi
- Department of Medical Laboratory Technology, College of Nursing and Health Science, Jazan University, Jazan 45142, Saudi Arabia
- Health Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Sabine Matou-Nasri
- Blood and Cancer Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh 11481, Saudi Arabia;
- Biosciences Department, Faculty of the School for Systems Biology, George Mason University, Manassas, VA 22030, USA
| | - Shmoukh Alotaibi
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia; (S.A.); (Y.M.H.)
| | - Yousef M. Hawsawi
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia; (S.A.); (Y.M.H.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Al-Faisal University, Riyadh 11533, Saudi Arabia
| | | | | | - Mohammed A. Jeraiby
- Department of Basic Medical Science, Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia;
| | - Ahmed A. Sulayli
- Laboratory Department, Prince Mohammed bin Nasser Hospital, Jazan Health Cluster, Jazan 82734, Saudi Arabia;
| | - Hassan N. Moafa
- Department of Public Health, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Department of Quality and Patients Safety, Jazan University Hospital, Jazan University, Jazan 45142, Saudi Arabia
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Kodumuru R, Sarkar S, Parepally V, Chandarana J. Artificial Intelligence and Internet of Things Integration in Pharmaceutical Manufacturing: A Smart Synergy. Pharmaceutics 2025; 17:290. [PMID: 40142954 PMCID: PMC11944607 DOI: 10.3390/pharmaceutics17030290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 02/14/2025] [Accepted: 02/16/2025] [Indexed: 03/28/2025] Open
Abstract
Background: The integration of artificial intelligence (AI) with the internet of things (IoTs) represents a significant advancement in pharmaceutical manufacturing and effectively bridges the gap between digital and physical worlds. With AI algorithms integrated into IoTs sensors, there is an improvement in the production process and quality control for better overall efficiency. This integration facilitates enabling machine learning and deep learning for real-time analysis, predictive maintenance, and automation-continuously monitoring key manufacturing parameters. Objective: This paper reviews the current applications and potential impacts of integrating AI and the IoTs in concert with key enabling technologies like cloud computing and data analytics, within the pharmaceutical sector. Results: Applications discussed herein focus on industrial predictive analytics and quality, underpinned by case studies showing improvements in product quality and reductions in downtime. Yet, many challenges remain, including data integration and the ethical implications of AI-driven decisions, and most of all, regulatory compliance. This review also discusses recent trends, such as AI in drug discovery and blockchain for data traceability, with the intent to outline the future of autonomous pharmaceutical manufacturing. Conclusions: In the end, this review points to basic frameworks and applications that illustrate ways to overcome existing barriers to production with increased efficiency, personalization, and sustainability.
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Affiliation(s)
| | | | - Varun Parepally
- Chemical Engineering Department, Michigan Technological University, Houghton, MI 49931, USA;
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Khorasani MA, Naghib SM. A review of chitosan-based multifunctional nanocomposites for drug/gene/protein delivery and gene therapy in cancer treatments: Promises, challenges and outlooks. Int J Biol Macromol 2025; 306:141394. [PMID: 39993690 DOI: 10.1016/j.ijbiomac.2025.141394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 02/06/2025] [Accepted: 02/20/2025] [Indexed: 02/26/2025]
Abstract
This study provides a comprehensive examination of chitosan-based multifunctional nanocomposites and their extensive applications in drug/gene/protein delivery, tissue engineering and cancer therapy. As a natural polymer with eco-friendly characteristics and both antimicrobial and anti-cancer properties, chitosan has garnered attention in numerous medical and pharmaceutical domains. The research explores diverse chitosan nanocomposites, including those incorporating magnetic nanoparticles, carbon nanotubes, and clay- and alginate-based nanocomposites. Additionally, the study addresses the obstacles encountered in developing these materials and their potential for creating advanced drug delivery systems and targeted treatments. The study highlights the applications of these nanocomposites in bone, cartilage, and skin tissue regeneration, as well as their potential in neural tissue engineering. in conclusion, the research underscores the promising future of chitosan-based nanocomposites in revolutionizing drug delivery, tissue engineering, and cancer therapy. It emphasizes the need for further studies to fully harness the potential of these materials and translate laboratory findings into clinical applications, paving the way for more effective and personalized medical treatments. Our reason for writing this article appears to be a comprehensive exploration of the potential and challenges of chitosan-based multifunctional nanocomposites in medicine, particularly in drug/gene/protein delivery and cancer therapy. The aim is to provide a detailed analysis of the material's versatility, its integration with advanced nanotechnologies, and its applications in targeted treatments, and regenerative medicine. we seek to address existing challenges, such as safety, scalability, and regulatory compliance, while highlighting the promising future of these materials in personalized and efficient medical treatments.
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Affiliation(s)
- Mohammad Ali Khorasani
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran.
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Rui M, Su Y, Tang H, Li Y, Fang N, Ge Y, Feng Q, Feng C. Computational Design and Optimization of Multi-Compound Multivesicular Liposomes for Co-Delivery of Traditional Chinese Medicine Compounds. AAPS PharmSciTech 2025; 26:61. [PMID: 39934607 DOI: 10.1208/s12249-025-03042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 01/08/2025] [Indexed: 02/13/2025] Open
Abstract
Study explored the synergistic anti-tumor effects of a combination of compounds from Traditional Chinese Medicine, including rosmarinic acid (RA), chlorogenic acid (CA), and scoparone (SCO), in the formulation of multivesicular liposomes (MVLs). Optimization of formulations and process parameters was essential to achieve effective liposomal encapsulation and optimal release profiles for these three compounds with diverse properties. Traditional trial-and-error approaches are inefficient for the optimization of complex multi-compound MVLs. We developed a new formulation optimization model, which could address this issue by predicting the optimal multi-compound MVLs formulation. Our machine learning model integrated support vector machine regression (SVR) algorithm and cuckoo search (CS) algorithm, resulting in three CS-SVR models to predict single-compound MVLs. The CS algorithm, with various weighting rules, was then applied to search the best formulation parameters across three CS-SVR models and to maximize the encapsulation efficiency for all three compounds. The multi-compound MLVs were subsequently prepared under the predicted conditions, achieving an optimized particle size of 15.12 µm, with encapsulation efficiencies of 82.93 ± 2.43% for CA, 82.22 ± 1.25% for RA, and 95.60 ± 0.18% for SCO. The predicted optimal multi-compound MVLs were further validated through in vitro characterization and in vivo anti-tumor experiments, showing a promising synergistic anti-tumor effect consistent with in vitro results. This model accurately predicted optimal encapsulation conditions, which were validated experimentally, demonstrating improved encapsulation efficiencies and reduced trial-and-error iterations. Collectively, our model provides a predictive pathway for multi-compound MVLs formulation, indicating the ability of this model to significantly reduce experimental burden and accelerate formulation development.
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Affiliation(s)
- Mengjie Rui
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Yali Su
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Haidan Tang
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Yinfeng Li
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Naying Fang
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Yingying Ge
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Qiuqi Feng
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China
| | - Chunlai Feng
- Department of Obstetrics, Affiliated Hospital of Jiangsu University, No.438 Jiefang Road, Zhenjiang, 212001, Jiangsu Province, China.
- School of Pharmacy, Jiangsu University, No.301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, China.
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Pal S, Nance KD, Joshi DR, Kales SC, Ye L, Hu X, Shamim K, Zakharov AV. Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors. J Chem Inf Model 2025; 65:1338-1356. [PMID: 39818814 DOI: 10.1021/acs.jcim.4c02126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2025]
Abstract
The global impact of SARS-CoV-2 highlights the need for treatments beyond vaccination, given the limited availability of effective medications. While Pfizer introduced Paxlovid, an FDA-approved antiviral targeting the SARS-CoV-2 main protease (Mpro), this study focuses on designing new antivirals against another protease, papain-like protease (PLpro), which is crucial for viral replication and immune suppression. NCATS/NIH performed a high-throughput screen of ∼15,000 molecules from an internal molecular library, identifying initial hits with a 0.5% success rate. To improve the hit rate and identify potent inhibitors, machine learning-based virtual screens were applied to ∼150,000 compounds, yielding 125 top predicted hits. Biochemical evaluation revealed 25 promising compounds, with a 20% hit-rate and IC50 values from 1.75 μM to <36 μM across 13 chemotypes. Further analog screening of those chemotypes, as part of the structure-activity relationships, led to 20 additional hits. Additionally, the hit-to-lead optimization of chemotype 7 produced 10 more analogs. These PLpro inhibitors provide promising templates for antiviral development against COVID-19.
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Affiliation(s)
- Sourav Pal
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Kellie D Nance
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Dirgha Raj Joshi
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Stephen C Kales
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Lin Ye
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Xin Hu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Khalida Shamim
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
| | - Alexey V Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, Maryland 20850, United States
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Alanazi M, Alanazi J, Alharby TN, Huwaimel B. Correlation of rivaroxaban solubility in mixed solvents for optimization of solubility using machine learning analysis and validation. Sci Rep 2025; 15:4725. [PMID: 39922955 PMCID: PMC11807219 DOI: 10.1038/s41598-025-89093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Accepted: 02/03/2025] [Indexed: 02/10/2025] Open
Abstract
In this study, the solubility of rivaroxaban, a poorly water-soluble drug, was investigated in mixed solvent systems to address challenges in pharmaceutical formulation and bioavailability enhancement. Solubility optimization is essential for the effective delivery and therapeutic performance of rivaroxaban, as its low aqueous solubility limits oral bioavailability and necessitates innovative approaches for drug formulation. The study explored the role of primary alcohols combined with dichloromethane in improving solubility, emphasizing their industrial relevance in crystallization, purification, and drug manufacturing processes. To complement experimental insights, machine learning models were employed to predict rivaroxaban solubility based on temperature, solvent type, and mass fraction of dichloromethane. Three models-AdaBoost Gaussian process regression (ADAGPR), AdaBoost multilayer perceptron (ADAMLP), and AdaBoost LASSO regression (ADALASSO)-were evaluated using [Formula: see text], RMSE, and MAPE metrics. Among these, ADAGPR demonstrated superior performance with an R² score of [Formula: see text], outperforming ADAMLP [Formula: see text] and [Formula: see text]. It also achieved the lowest total RMSE [Formula: see text] and MAPE [Formula: see text], confirming its predictive precision and reliability. Optimal solubility conditions were identified at [Formula: see text] with a mass fraction of 0.8190 in a dichloromethane-methanol mixture, yielding a predicted solubility of [Formula: see text]. These findings highlight the potential of combining chemical engineering principles with advanced predictive modeling to optimize solubility in complex solvent systems, offering significant value to pharmaceutical development and process optimization.
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Affiliation(s)
- Muteb Alanazi
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha'il, Ha'il, 81442, Saudi Arabia.
| | - Jowaher Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Ha'il, Ha'il, 81442, Saudi Arabia
| | - Tareq Nafea Alharby
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha'il, Ha'il, 81442, Saudi Arabia
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Ha'il, Hail, 81442, Saudi Arabia
- Medical and Diagnostic Research Center, University of Ha'il, Hail, 55473, Saudi Arabia
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Smeu A, Marcovici I, Dehelean CA, Dumitrel SI, Borza C, Lighezan R. Flavonoids and Flavonoid-Based Nanopharmaceuticals as Promising Therapeutic Strategies for Colorectal Cancer-An Updated Literature Review. Pharmaceuticals (Basel) 2025; 18:231. [PMID: 40006045 PMCID: PMC11858883 DOI: 10.3390/ph18020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 02/04/2025] [Accepted: 02/05/2025] [Indexed: 02/27/2025] Open
Abstract
Colorectal cancer (CRC) represents one of the most serious health issues and the third most commonly diagnosed cancer worldwide. However, the treatment options for CRC are associated with adverse reactions, and in some cases, resistance can develop. Flavonoids have emerged as promising alternatives for CRC prevention and therapy due to their multitude of biological properties and ability to target distinct processes involved in CRC pathogenesis. Their innate disadvantageous properties (e.g., low solubility and stability, reduced bioavailability, and lack of tumor specificity) have delayed the potential inclusion of flavonoids in CRC treatment regimens but have hastened the design of nanopharmaceuticals comprising a flavonoid agent entrapped in a nanosized delivery platform that not only counteract these inconveniences but also provide an augmented therapeutic effect and an elevated safety profile by conferring a targeted action. Starting with a brief presentation of the pathological features of CRC and an overview of flavonoid classes, the present study comprehensively reviews the anti-CRC activity of different flavonoids from a mechanistic perspective while also portraying the latest discoveries made in the area of flavonoid-containing nanocarriers that have proved efficient in CRC management. This review concludes by showcasing future perspectives for the advancement of flavonoids and flavonoid-based nanopharmaceuticals in CRC research.
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Affiliation(s)
- Andreea Smeu
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Iasmina Marcovici
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Cristina Adriana Dehelean
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Stefania-Irina Dumitrel
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Claudia Borza
- Department of Functional Sciences, Discipline of Pathophysiology, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timișoara, Romania
- Centre for Translational Research and Systems Medicine, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timișoara, Romania
- Centre of Cognitive Research in Pathological Neuro-Psychiatry NEUROPSY-COG, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Rodica Lighezan
- Center for Diagnosis and Study of Parasitic Diseases, Department of Infectious Disease, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Discipline of Parasitology, Department of Infectious Diseases, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
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Das SK, Mishra R, Samanta A, Shil D, Roy SD. Deep learning: A game changer in drug design and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2025; 103:101-120. [PMID: 40175037 DOI: 10.1016/bs.apha.2025.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2025]
Abstract
The lengthy and costly drug discovery process is transformed by deep learning, a subfield of artificial intelligence. Deep learning technologies expedite the procedure, increasing treatment success rates and speeding life-saving procedures. Deep learning stands out in target identification and lead selection. Deep learning greatly accelerates initial stage by analyzing large datasets of biological data to identify possible therapeutic targets and rank targeted drug molecules with desired features. Predicting possible adverse effects is another significant challenge. Deep learning offers prompt and efficient assistance with toxicology prediction in a very short time, deep learning algorithms can forecast a new drug's possible harm. This enables to concentrate on safer alternatives and steer clear of late-stage failures brought on by unanticipated toxicity. Deep learning unlocks the possibility of drug repurposing; by examining currently available medications, it is possible to find whole new therapeutic uses. This method speeds up development of diseases that were previously incurable. De novo drug discovery is made possible by deep learning when combined with sophisticated computational modeling, it can create completely new medications from the ground. Deep learning can recommend and direct towards new drug candidates with high binding affinities and intended therapeutic effects by examining molecular structures of disease targets. This provides focused and personalized medication. Lastly, drug characteristics can be optimized with aid of deep learning. Researchers can create medications with higher bioavailability and fewer toxicity by forecasting drug pharmacokinetics. In conclusion, deep learning promises to accelerate drug development, reduce costs, and ultimately save lives.
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Affiliation(s)
- Sushanta Kumar Das
- Mata Gujri College of Pharmacy, Mata Gujri University, Kishanganj, Bihar, India.
| | - Rahul Mishra
- Pharmacokinetics Scientist, Phase 1 Clinical Trial, Celerion IMC, Rose Street, Lincoln, NE, United States
| | - Amit Samanta
- Mata Gujri College of Pharmacy, Mata Gujri University, Kishanganj, Bihar, India
| | - Dibyendu Shil
- Mata Gujri College of Pharmacy, Mata Gujri University, Kishanganj, Bihar, India
| | - Saumendu Deb Roy
- Mata Gujri College of Pharmacy, Mata Gujri University, Kishanganj, Bihar, India
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Bhowmick M, Goswami S, Bhowmick P, Hait S, Rath D, Yasmin S. Future prospective of AI in drug discovery. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2025; 103:429-449. [PMID: 40175053 DOI: 10.1016/bs.apha.2025.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2025]
Abstract
Drug discovery and development is very expensive and long with an inferior success rate. It is quite inefficient and costly due to huge R&D costs and lower productivity in pharmaceutical industries, to discover effective drugs and their development. AI can revolutionize the history of drug discovery and development because it will solve all these problems. AI can identify some promising drug candidates, reduce costs, and increase precision. AI algorithms analyze large datasets, predict molecular interactions, and help optimize the design of clinical trials, making the process of drug discovery and biomedical research much more efficient. By combining cutting-edge computation with more conventional pharmaceutical strategy, AI aids in expediting the process of therapeutics development. This chapter is an investigation of the core reasons behind lower approval rates of new drugs, the potential scope of AI to improve the drug discovery and development scenario, and the practical applications in the field. This article will further explore future opportunities, key methodologies, and challenges in the implementation of AI in pharmaceutical research.
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Affiliation(s)
- Mithun Bhowmick
- Bengal College of Pharmaceutical Sciences and Research, Durgapur, West Bengal, India.
| | - Sourajyoti Goswami
- Bengal College of Pharmaceutical Sciences and Research, Durgapur, West Bengal, India
| | - Pratibha Bhowmick
- Bengal College of Pharmaceutical Sciences and Research, Durgapur, West Bengal, India
| | - Santanu Hait
- Bengal College of Pharmaceutical Sciences and Research, Durgapur, West Bengal, India
| | - Dipayan Rath
- Bengal College of Pharmaceutical Sciences and Research, Durgapur, West Bengal, India
| | - Sabina Yasmin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Asir-Abha, Saudi Arabia
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Alberts A, Bratu AG, Niculescu AG, Grumezescu AM. New Perspectives of Hydrogels in Chronic Wound Management. Molecules 2025; 30:686. [PMID: 39942790 PMCID: PMC11820815 DOI: 10.3390/molecules30030686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 01/29/2025] [Accepted: 01/31/2025] [Indexed: 02/16/2025] Open
Abstract
Chronic wounds pose a substantial healthcare concern due to their prevalence and cost burden. This paper presents a detailed overview of chronic wounds and emphasizes the critical need for novel therapeutic solutions. The pathophysiology of wound healing is discussed, including the healing stages and the factors contributing to chronicity. The focus is on diverse types of chronic wounds, such as diabetic foot necrosis, pressure ulcers, and venous leg ulcers, highlighting their etiology, consequences, and the therapeutic issues they provide. Further, modern wound care solutions, particularly hydrogels, are highlighted for tackling the challenges of chronic wound management. Hydrogels are characterized as multipurpose materials that possess vital characteristics like the capacity to retain moisture, biocompatibility, and the incorporation of active drugs. Hydrogels' effectiveness in therapeutic applications is demonstrated by how they support healing, including preserving ideal moisture levels, promoting cellular migration, and possessing antibacterial properties. Thus, this paper presents hydrogel technology's latest developments, emphasizing drug-loaded and stimuli-responsive types and underscoring how these advanced formulations greatly improve therapy outcomes by enabling dynamic and focused reactions to the wound environment. Future directions for hydrogel research promote the development of customized hydrogel treatments and the incorporation of digital health tools to improve the treatment of chronic wounds.
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Affiliation(s)
- Adina Alberts
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Andreea Gabriela Bratu
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.G.B.); (A.-G.N.)
| | - Adelina-Gabriela Niculescu
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.G.B.); (A.-G.N.)
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
| | - Alexandru Mihai Grumezescu
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, Gh. Polizu St. 1-7, 060042 Bucharest, Romania; (A.G.B.); (A.-G.N.)
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
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Albayati N, Talluri SR, Dholaria N, Michniak-Kohn B. AI-Driven Innovation in Skin Kinetics for Transdermal Drug Delivery: Overcoming Barriers and Enhancing Precision. Pharmaceutics 2025; 17:188. [PMID: 40006555 PMCID: PMC11859831 DOI: 10.3390/pharmaceutics17020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Revised: 01/19/2025] [Accepted: 01/30/2025] [Indexed: 02/27/2025] Open
Abstract
Transdermal drug delivery systems (TDDS) offer an alternative to conventional oral and injectable drug administration by bypassing the gastrointestinal tract and liver metabolism, improving bioavailability, and minimizing systemic side effects. However, widespread adoption of TDDS is limited by challenges such as the skin's permeability barrier, particularly the stratum corneum, and the need for optimized formulations. Factors like skin type, hydration levels, and age further complicate the development of universally effective solutions. Advances in artificial intelligence (AI) address these challenges through predictive modeling and personalized medicine approaches. Machine learning models trained on extensive molecular datasets predict skin permeability and accelerate the selection of suitable drug candidates. AI-driven algorithms optimize formulations, including penetration enhancers and advanced delivery technologies like microneedles and liposomes, while ensuring safety and efficacy. Personalized TDDS design tailors drug delivery to individual patient profiles, enhancing therapeutic precision. Innovative systems, such as sensor-integrated patches, dynamically adjust drug release based on real-time feedback, ensuring optimal outcomes. AI also streamlines the pharmaceutical process, from disease diagnosis to the prediction of drug distribution in skin layers, enabling efficient formulation development. This review highlights AI's transformative role in TDDS, including applications of models such as Deep Neural Networks (DNN), Artificial Neural Networks (ANN), BioSIM, COMSOL, K-Nearest Neighbors (KNN), and Set Covering Machine (SVM). These technologies revolutionize TDDS for both skin and non-skin diseases, demonstrating AI's potential to overcome existing barriers and improve patient care through innovative drug delivery solutions.
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Affiliation(s)
- Nubul Albayati
- Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA; (N.A.); (S.R.T.); (N.D.)
- Center for Dermal Research, Rutgers-The State University of New Jersey, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Sesha Rajeswari Talluri
- Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA; (N.A.); (S.R.T.); (N.D.)
- Center for Dermal Research, Rutgers-The State University of New Jersey, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Nirali Dholaria
- Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA; (N.A.); (S.R.T.); (N.D.)
- Center for Dermal Research, Rutgers-The State University of New Jersey, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Bozena Michniak-Kohn
- Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA; (N.A.); (S.R.T.); (N.D.)
- Center for Dermal Research, Rutgers-The State University of New Jersey, 145 Bevier Road, Piscataway, NJ 08854, USA
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Bao Y, Ma Y, Huang W, Bai Y, Gao S, Xiu L, Xie Y, Wan X, Shan S, Chen C, Qu L. Regulation of autophagy and cellular signaling through non-histone protein methylation. Int J Biol Macromol 2025; 291:139057. [PMID: 39710032 DOI: 10.1016/j.ijbiomac.2024.139057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 12/06/2024] [Accepted: 12/19/2024] [Indexed: 12/24/2024]
Abstract
Autophagy is a highly conserved catabolic pathway that is precisely regulated and plays a significant role in maintaining cellular metabolic balance and intracellular homeostasis. Abnormal autophagy is directly linked to the development of various diseases, particularly immune disorders, neurodegenerative conditions, and tumors. The precise regulation of proteins is crucial for proper cellular function, and post-translational modifications (PTMs) are key epigenetic mechanisms in the regulation of numerous biological processes. Multiple proteins undergo PTMs that influence autophagy regulation. Methylation modifications on non-histone lysine and arginine residues have been identified as common PTMs critical to various life processes. This paper focused on the regulatory effects of non-histone methylation modifications on autophagy, summarizing related research on signaling pathways involved in autophagy-related non-histone methylation, and discussing current challenges and clinical significance. Our review concludes that non-histone methylation plays a pivotal role in the regulation of autophagy and its associated signaling pathways. Targeting non-histone methylation offers a promising strategy for therapeutic interventions in diseases related to autophagy dysfunction, such as cancer and neurodegenerative disorders. These findings provide a theoretical basis for the development of non-histone-methylation-targeted drugs for clinical use.
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Affiliation(s)
- Yongfen Bao
- Hubei Key Laboratory of Diabetes and Angiopathy, School of Pharmacy, Hubei University of Science and Technology, Xianning 437000, China; School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, China
| | - Yaoyao Ma
- Hubei Key Laboratory of Diabetes and Angiopathy, School of Pharmacy, Hubei University of Science and Technology, Xianning 437000, China; School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, China
| | - Wentao Huang
- Department of Physiology, Hunan Normal University School of Medicine, Changsha 410013, China
| | - Yujie Bai
- Department of Scientific Research and Education, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330000, China
| | - Siying Gao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Luyao Xiu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yuyang Xie
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinrong Wan
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shigang Shan
- School of Public Health and Nursing, Hubei University of Science and Technology, Hubei 437000, China
| | - Chao Chen
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lihua Qu
- Hubei Key Laboratory of Diabetes and Angiopathy, School of Pharmacy, Hubei University of Science and Technology, Xianning 437000, China; School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, China.
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Caddeo A, Romeo S. Precision medicine and nucleotide-based therapeutics to treat steatotic liver disease. Clin Mol Hepatol 2025; 31:S76-S93. [PMID: 39103998 PMCID: PMC11925435 DOI: 10.3350/cmh.2024.0438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/31/2024] [Accepted: 08/04/2024] [Indexed: 08/07/2024] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a complex multifactorial disease and becoming the leading cause of liver-related morbidity and mortality. MASLD spans from isolated steatosis to metabolic dysfunction-associated steatohepatitis (MASH), that may progress to cirrhosis and hepatocellular carcinoma (HCC). Genetic, metabolic, and environmental factors strongly contribute to the heterogeneity of MASLD. Lifestyle intervention and weight loss represent a viable treatment for MASLD. Moreover, Resmetirom, a thyroid hormone beta receptor agonist, has recently been approved for MASLD treatment. However, most individuals treated did not respond to this therapeutic, suggesting the need for a more tailored approach to treat MASLD. Oligonucleotide-based therapies, namely small-interfering RNA (siRNA) and antisense oligonucleotide (ASO), have been recently developed to tackle MASLD by reducing the expression of genes influencing MASH progression, such as PNPLA3 and HSD17B13. Here, we review the latest progress made in the synthesis and development of oligonucleotide-based agents targeting genetic determinants of MASH.
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Affiliation(s)
- Andrea Caddeo
- Department of Biomedical Sciences, Unit of Oncology and Molecular Pathology, University of Cagliari, Cagliari, Italy
| | - Stefano Romeo
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, University Magna Graecia, Catanzaro, Italy
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Medicine, Endocrinology (H7) Karolinska Institute and Hospital, Huddinge, Stockholm, Sweden
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Alemu R, Sharew NT, Arsano YY, Ahmed M, Tekola-Ayele F, Mersha TB, Amare AT. Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues. Hum Genomics 2025; 19:8. [PMID: 39891174 PMCID: PMC11786457 DOI: 10.1186/s40246-025-00718-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 01/16/2025] [Indexed: 02/03/2025] Open
Abstract
Non-communicable diseases (NCDs) such as cardiovascular diseases, chronic respiratory diseases, cancers, diabetes, and mental health disorders pose a significant global health challenge, accounting for the majority of fatalities and disability-adjusted life years worldwide. These diseases arise from the complex interactions between genetic, behavioral, and environmental factors, necessitating a thorough understanding of these dynamics to identify effective diagnostic strategies and interventions. Although recent advances in multi-omics technologies have greatly enhanced our ability to explore these interactions, several challenges remain. These challenges include the inherent complexity and heterogeneity of multi-omic datasets, limitations in analytical approaches, and severe underrepresentation of non-European genetic ancestries in most omics datasets, which restricts the generalizability of findings and exacerbates health disparities. This scoping review evaluates the global landscape of multi-omics data related to NCDs from 2000 to 2024, focusing on recent advancements in multi-omics data integration, translational applications, and equity considerations. We highlight the need for standardized protocols, harmonized data-sharing policies, and advanced approaches such as artificial intelligence/machine learning to integrate multi-omics data and study gene-environment interactions. We also explore challenges and opportunities in translating insights from gene-environment (GxE) research into precision medicine strategies. We underscore the potential of global multi-omics research in advancing our understanding of NCDs and enhancing patient outcomes across diverse and underserved populations, emphasizing the need for equity and fairness-centered research and strategic investments to build local capacities in underrepresented populations and regions.
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Affiliation(s)
- Robel Alemu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Anderson School of Management, University of California Los Angeles, Los Angeles, CA, USA.
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.
| | - Nigussie T Sharew
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Yodit Y Arsano
- Alpert Medical School, Lifespan Health Systems, Brown University, WarrenProvidence, Rhode Island, USA
| | - Muktar Ahmed
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tesfaye B Mersha
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Azmeraw T Amare
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.
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Steyn JD, Haasbroek-Pheiffer A, Pheiffer W, Weyers M, van Niekerk SE, Hamman JH, van Staden D. Evaluation of Drug Permeation Enhancement by Using In Vitro and Ex Vivo Models. Pharmaceuticals (Basel) 2025; 18:195. [PMID: 40006008 PMCID: PMC11859300 DOI: 10.3390/ph18020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 01/23/2025] [Accepted: 01/29/2025] [Indexed: 02/27/2025] Open
Abstract
Drugs administered by means of extravascular routes of drug administration must be absorbed into the systemic circulation, which involves the movement of the drug molecules across biological barriers such as epithelial cells that cover mucosal surfaces or the stratum corneum that covers the skin. Some drugs exhibit poor permeation across biological membranes or may experience excessive degradation during first-pass metabolism, which tends to limit their bioavailability. Various strategies have been used to improve drug bioavailability. Absorption enhancement strategies include the co-administration of chemical permeation enhancers, enzymes, and/or efflux transporter inhibitors, chemical changes, and specialized dosage form designs. Models with physiological relevance are needed to evaluate the efficacy of drug absorption enhancement techniques. Various in vitro cell culture models and ex vivo tissue models have been explored to evaluate and quantify the effectiveness of drug permeation enhancement strategies. This review deliberates on the use of in vitro and ex vivo models for the evaluation of drug permeation enhancement strategies for selected extravascular drug administration routes including the nasal, oromucosal, pulmonary, oral, rectal, and transdermal routes of drug administration.
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Affiliation(s)
- Johan D. Steyn
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2531, South Africa; (J.D.S.); (A.H.-P.); (M.W.); (S.E.v.N.); (J.H.H.)
| | - Anja Haasbroek-Pheiffer
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2531, South Africa; (J.D.S.); (A.H.-P.); (M.W.); (S.E.v.N.); (J.H.H.)
| | - Wihan Pheiffer
- Preclinical Drug Development Platform, Faculty of Health Sciences, North-West University, Potchefstroom 2531, South Africa;
| | - Morné Weyers
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2531, South Africa; (J.D.S.); (A.H.-P.); (M.W.); (S.E.v.N.); (J.H.H.)
| | - Suzanne E. van Niekerk
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2531, South Africa; (J.D.S.); (A.H.-P.); (M.W.); (S.E.v.N.); (J.H.H.)
| | - Josias H. Hamman
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2531, South Africa; (J.D.S.); (A.H.-P.); (M.W.); (S.E.v.N.); (J.H.H.)
| | - Daniélle van Staden
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2531, South Africa; (J.D.S.); (A.H.-P.); (M.W.); (S.E.v.N.); (J.H.H.)
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Młynarska E, Bojdo K, Frankenstein H, Kustosik N, Mstowska W, Przybylak A, Rysz J, Franczyk B. Nanotechnology and Artificial Intelligence in Dyslipidemia Management-Cardiovascular Disease: Advances, Challenges, and Future Perspectives. J Clin Med 2025; 14:887. [PMID: 39941558 PMCID: PMC11818864 DOI: 10.3390/jcm14030887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 01/11/2025] [Accepted: 01/27/2025] [Indexed: 02/16/2025] Open
Abstract
This narrative review explores emerging technologies in dyslipidemia management, focusing on nanotechnology and artificial intelligence (AI). It examines the current treatment recommendations and contrasts them with the future prospects enabled by these innovations. Nanotechnology shows significant potential in enhancing drug delivery systems, enabling more targeted and efficient lipid-lowering therapies. In parallel, AI offers advancements in diagnostics, cardiovascular risk prediction, and personalized treatment strategies. AI-based decision support systems and machine learning algorithms are particularly promising for analyzing large datasets and delivering evidence-based recommendations. Together, these technologies hold the potential to revolutionize dyslipidemia management, improving outcomes and optimizing patient care. In addition, this review covers key topics such as cardiovascular disease biomarkers and risk factors, providing insights into the current methods for assessing cardiovascular risk. It also discusses the current understanding of dyslipidemia, including pathophysiology and clinical management. Together, these insights and technologies hold the potential to revolutionize dyslipidemia management, improving outcomes and optimizing patient care.
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Affiliation(s)
- Ewelina Młynarska
- Department of Nephrocardiology, Medical University of Lodz, 90-549 Łódź, Poland
| | - Kinga Bojdo
- Department of Nephrocardiology, Medical University of Lodz, 90-549 Łódź, Poland
| | - Hanna Frankenstein
- Department of Nephrocardiology, Medical University of Lodz, 90-549 Łódź, Poland
| | - Natalia Kustosik
- Department of Nephrocardiology, Medical University of Lodz, 90-549 Łódź, Poland
| | - Weronika Mstowska
- Department of Nephrocardiology, Medical University of Lodz, 90-549 Łódź, Poland
| | | | - Jacek Rysz
- Department of Nephrology, Hypertension and Internal Medicine, Medical University of Lodz, 90-549 Łodz, Poland
| | - Beata Franczyk
- Department of Nephrocardiology, Medical University of Lodz, 90-549 Łódź, Poland
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