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Omics-Driven Unveiling of the Structure and Function of Nanoparticles

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 4435

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Guest Editor
Department of Pharmacy, University of Naples Federico II, Via Tommaso De Amicis 95, 80131 Naples, Italy
Interests: functional proteomics; global proteomics; drug target deconvolution; mass spectrometry; biochemistry; marine bioactive compounds; nanoparticle protein corona; metabolomics; metabolite quantification
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Special Issue Information

Dear Colleagues,

Nanoparticles (NPs) are chemical entities endowed with enhanced physical and chemical characteristics, due to their lower-than-100 nm dimensions and tunable surface properties. Thus, NPs have great success in a wide variety of fields, such as in medicinal, environmental, and energy-based research, as well as in imaging and in biochemical sensing. In the biomedical area, NP-based formulations hold great promise, being particularly suited for the delivery of biomolecules and drugs, thus allowing for the development of targeted therapies for precision medicine. When administrated, upon exposure to complex biological environments, NPs quickly form a layer of adsorbed biomolecules, called the biomolecular corona. This dynamic structure comprises lipids, sugars, nucleic acids, and, mostly, proteins. After its formation, the corona dictates the fate and function of the NPs inside the body. As such, a thorough characterization of the physical and chemical properties of NPs, as well as of the biomolecular corona they acquire in different biological contexts, appears fundamental for the design of tunable delivery systems. In this scenario, omics-based approaches appear as a powerful tool for a comprehensive understanding of NPs’ properties and potential. Thus, this Special Issue welcomes both original research and review papers devoted to the characterization of the structure and function of NPs through omics strategies.

Dr. Elva Morretta
Guest Editor

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Keywords

  • nanoparticles
  • nanotechnology
  • drug delivery
  • protein corona
  • proteomics
  • nano-proteomics
  • matabolomics
  • lipidomics

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Published Papers (3 papers)

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Research

19 pages, 10505 KB  
Article
Cellular Metabolic Responses to Copper Nanoparticles: Comparison Between Normal and Breast Cancer Cells
by Alexandra Ivan, Maria-Alexandra Pricop, Alexandra Teodora Lukinich-Gruia, Iustina-Mirabela Cristea, Adina Negrea, Ioan Bogdan Pascu, Crenguta Livia Calma, Andreea Paunescu, Virgil Paunescu and Calin Adrian Tatu
Int. J. Mol. Sci. 2025, 26(21), 10716; https://doi.org/10.3390/ijms262110716 - 4 Nov 2025
Viewed by 401
Abstract
The use of copper nanoparticles (CuNPs) seems to be an alternative therapeutic strategy for cancer therapy due to low-cost synthesis and anticancer activity. In this work, CuNPs’ effects were tested in various concentrations on two types of cells: mesenchymal stem cells (MSCs) and [...] Read more.
The use of copper nanoparticles (CuNPs) seems to be an alternative therapeutic strategy for cancer therapy due to low-cost synthesis and anticancer activity. In this work, CuNPs’ effects were tested in various concentrations on two types of cells: mesenchymal stem cells (MSCs) and a breast cancer cell line, SKBR3. The concentrations (0.25 mM, 0.5 mM, 1 mM and 2 mM) were first tested on an impedance-based cytotoxicity assay and then used in further cellular metabolic assays. Next, several techniques were applied to test the chosen concentrations: assessment of apoptosis, intracellular reactive oxygen species (ROS) levels, oxidative stress-related gene expression, assessment of mitochondrial respiration and fatty acid methyl ester (FAME) profile evaluation. The higher CuNP concentrations tested on the SKBR3 cell line showed a dose-dependent decrease in the cell index. SKBR3 cells displayed increased CAT and SOD expression, revealed by strong dose-dependent fluorescence. Annexin/PI staining confirmed increased SKBR3 cell death induced by the higher doses of CuNPs. SKBR3 revealed higher baseline respiratory capacity compared to MSCs. Fatty acid methyl esters (FAMEs) are in higher abundance in MSCs compared to the SKBR3 cell line. The different metabolic response in the tested cells to the CuNPs’ presence could help establish a future personalized treatment for breast cancer patients. Full article
(This article belongs to the Special Issue Omics-Driven Unveiling of the Structure and Function of Nanoparticles)
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15 pages, 2391 KB  
Article
Human Serum Albumin-Based Nanoparticles for Targeted Intracellular Drug Delivery
by Claudia Gabriela Chilom, Sorina Iftimie, Adriana Elena Balan, Daniela Oprea, Monica Enculescu and Teodor Adrian Enache
Int. J. Mol. Sci. 2025, 26(17), 8297; https://doi.org/10.3390/ijms26178297 - 27 Aug 2025
Cited by 1 | Viewed by 1685
Abstract
We report the synthesis and characterization of folic acid (FA)-conjugated human serum albumin nanoparticles, (HSA-FA):Ru NPs, as targeted carriers for rutin (Ru), a flavonoid with known anticancer activity. Nanoparticles were fabricated via a desolvation method, and their surface was functionalized with folic acid [...] Read more.
We report the synthesis and characterization of folic acid (FA)-conjugated human serum albumin nanoparticles, (HSA-FA):Ru NPs, as targeted carriers for rutin (Ru), a flavonoid with known anticancer activity. Nanoparticles were fabricated via a desolvation method, and their surface was functionalized with folic acid to promote selective uptake by cancer cells overexpressing folate receptors. Morphological and dimensional analyses performed by atomic force microscopy (AFM), scanning electron microscopy (SEM), and fluorescence microscopy confirmed that all nanoparticles were below 100 nm and exhibited good colloidal stability. Voltametric measurements confirmed the successful incorporation of both rutin and folic acid within the (HSA-FA):Ru nanoparticle formulation. Biological evaluation was conducted on healthy L929 fibroblasts and HT-29 colon adenocarcinoma cells. MTS colorimetric assays revealed that (HSA-FA):Ru NPs significantly reduced the viability of HT-29 cells, while maintaining higher compatibility with L929 cells. Fluorescence and electron microscopy further confirmed preferential nanoparticle uptake and surface accumulation in HT-29 cells, supporting the role of folic acid in enhancing targeted delivery. The study demonstrates that HSA-based nanoparticles functionalized with FA and loaded with Ru offer a biocompatible and efficient strategy for selective intracellular drug delivery in colorectal cancer. These findings support the use of albumin-based nanocarriers in the development of targeted therapeutic platforms for cancer treatment. Full article
(This article belongs to the Special Issue Omics-Driven Unveiling of the Structure and Function of Nanoparticles)
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23 pages, 2510 KB  
Article
Variations in Circulating Tumor Microenvironment-Associated Proteins in Non-Muscle Invasive Bladder Cancer Induced by Mitomycin C Treatment
by Benito Blanco Gómez, Francisco Javier Casas-Nebra, Daniel Pérez-Fentes, Susana B. Bravo, Laura Rodríguez-Silva and Cristina Núñez
Int. J. Mol. Sci. 2025, 26(15), 7413; https://doi.org/10.3390/ijms26157413 - 1 Aug 2025
Viewed by 1693
Abstract
Mitomycin C (MMC) is a widely employed chemotherapeutic agent, particularly in non-muscle invasive bladder cancer (NMIBC), where it functions by inducing DNA cross-linking and promoting tumor cell apoptosis. However, the tumor microenvironment (TME) significantly influences the therapeutic efficacy of MMC. Among the key [...] Read more.
Mitomycin C (MMC) is a widely employed chemotherapeutic agent, particularly in non-muscle invasive bladder cancer (NMIBC), where it functions by inducing DNA cross-linking and promoting tumor cell apoptosis. However, the tumor microenvironment (TME) significantly influences the therapeutic efficacy of MMC. Among the key regulators within the TME, the complement system and the coagulation pathway play a crucial role in modulating immune responses to cancer therapies, including MMC. This article explores the interaction between platinum nanoparticles (PtNPs) with human serum (HS) of NMIBC patients (T1 and Ta subtypes) at three different points: before the chemotherapy instillation of MMC (t0) and three (t3) and six months (t6) after the treatment with MMC. This novel nanoproteomic strategy allowed the identification of a TME proteomic signature associated with the response to MMC treatment. Importantly, two proteins involved in the immune response were found to be deregulated across all patients (T1 and Ta subtypes) during MMC treatment: prothrombin (F2) downregulated and complement component C7 (C7) upregulated. By understanding how these biomarker proteins interact with MMC treatment, novel therapeutic strategies can be developed to enhance treatment outcomes and overcome resistance in NMIBC. Full article
(This article belongs to the Special Issue Omics-Driven Unveiling of the Structure and Function of Nanoparticles)
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