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25th Anniversary of IJMS: Updates and Advances in Molecular Nanoscience

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 2870

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Special Issue Editors

Dr. Qi Zhang

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Guest Editor

State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou 215125, China
Interests: nanomaterial-mediated stem cell for the repair of tissue injury; nanomaterial-mediated multi-modal imaging and chemo-radiotherapy

Dr. Marilena Carbone

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Guest Editor

Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
Interests: nanoparticles with electrochemical and biomedical applications; tattoo inks: determination of the composition and removal; surface science: molecules on semiconductors for detection purposes
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Dr. André F. Moreira

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1. BRIDGES-Biotechnology Research, Innovation and Design of Health Products, Polytechnic of Guarda, 6300-559 Guarda, Portugal
2. RISE-Health, Department of Medical Sciences, Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
Interests: biomaterials; tissue engineering; drug delivery; photothermal therapy; controlled drug release; nanomaterials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The collection of papers presented in this 25th anniversary Special Issue of the International Journal of Molecular Sciences features some of the most interesting developments in the field of Molecular Nanoscience. Over the last few decades, significant progress has been made in functional nanomaterials and the biology or life science application of nanomaterials. It is meaningful to investigate how the functional structure of materials influence biological performance in vitro and in vivo and how clinical requirements drive the design of new nanomaterials. Although many nanomaterials have been designed and synthesized over the years, with numerous reviews and articles exploring these topics, there is still a lack of in-depth investigation and a dedicated Special Issue on the biological effects of nanomaterials, particularly in fields of regenerative medicine, cellular therapy, radiology, and targeted therapy. This Special Issue also focuses on the development of specific approaches to study the biological application of 2D materials (i.e. graphene and nanosheets), covalent organic frameworks (COFs), metal–organic frameworks (MOFs), and the biological effects of smart nanomaterials, theranostic nanomaterials, nanocatalysts and nanozymes, and the computational biology of nanosystems.

We cordially invite scientists to contribute to this Special Issue, which aims to foster cutting-edge advancements in Molecular Nanoscience. As part of this Special Issue, we welcome submissions from researchers in the form of original research papers, communications, and review articles on, but not limited to, the following topics:

Functional nanomaterials

Design and synthesis or fabrication of functional nanomaterials and their applications in regenerative medicine, cellular therapy, radiology, and targeted therapy

Nanostructure of materials

Two-dimensional materials (i.e. graphene and nanosheets), covalent organic frameworks (COFs), and metal-organic frameworks (MOFs)

Bioimaging and responsiveness of nanomaterials

Smart nanomaterials (i.e., pH/ROS/immune response materials) and theranostic nanomaterials

Computational biology of nanosystems

Understanding the functions and behaviors of signal pathways, ion channels, and protein interactions from the perspective of computational biology and nanotechnology

Dr. Qi Zhang
Dr. Marilena Carbone
Dr. André F. Moreira
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

nanotechnology
nanomaterials
nanomedicine
nanostructures
2D materials
smart nanomaterials
nanocatalysts
nanozymes

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Published Papers (5 papers)

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Research

12 pages, 1301 KB

Open AccessArticle

Nanomaterials Covered with Cell Membranes for Intracellular Delivery Without Lysosomal Degradation and Innate Immunity Induction

by Olga Morozova, Ekaterina Obraztsova and Dmitry Klinov

Int. J. Mol. Sci. 2025, 26(20), 10244; https://doi.org/10.3390/ijms262010244 - 21 Oct 2025

Viewed by 290

Abstract

Cellular uptake of nanomaterials is based on endocytosis with their endosomal–lysosomal entrapment resulting in enzymatic hydrolysis. Besides biodegradation, the antigen presentation induces innate and adaptive immunity. Our goal was isolation of extracellular particles to study their structures, penetration into cells, stability, intracellular distribution, and interferon (IFN) production. Extracellular nanomaterials were isolated from conditioned culture media of human embryonic and cancer cells by two-stage differential centrifugation. Cellular uptake of Cy5-labeled particles was evaluated using spectrofluorimetry and confocal fluorescent microscopy. IFN gene expression was analyzed by reverse transcription with real-time PCR and ELISA. Vesicles of 10–200 nm were isolated by centrifugation at 20,800× g at +4 °C for 30 min. The fluorescent vesicles were gradually accumulated inside cells for seven days. Intracellular distribution patterns of the Cy5-labeled vesicles differed from lysosomes stained with LysoRed tracker. IFNs α, β and γ were not detected after treatment with the vesicles. IFN λ was found in cells in the presence of allogenic but not autologous particles. The gradual cellular uptake occurred without significant differences between autologous and heterologous vesicles. Different localization of the extracellular vesicles (EV) and lysosomes along with weak innate immune response (if any) suggested membrane fusion. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Nanoscience)

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18 pages, 2836 KB

Open AccessArticle

Silica Spheres Functionalized with Silver and Bismuth Nanoparticles—Antibacterial Activity Against Clinically Relevant Bacterial Pathogens

by Marcin Gajek, Karolina Klesiewicz, Maria Biegun-Żurowska, Paula Parreira, Magdalena Ziąbka, Agnieszka Różycka and Alicja Rapacz-Kmita

Int. J. Mol. Sci. 2025, 26(20), 10203; https://doi.org/10.3390/ijms262010203 - 20 Oct 2025

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Abstract

The aim of the study was to develop hybrid nanomaterials based on monodisperse silica spheres as carriers for silver nanoparticles (AgNPs) or bismuth nanoparticles (BiNPs) and to evaluate their antimicrobial properties. Silica spheres were synthesized using a modified Stöber method, either unmodified or functionalized with (3-aminopropyl)triethoxysilane (APTES), prior to AgNP or BiNP deposition. The materials were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), inductively coupled plasma optical emission spectroscopy (ICP-OES), and zeta potential measurements, while antimicrobial activity was assessed by microdilution against Gram-positive (Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Enterococcus faecium) and Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa), with Helicobacter pylori as a clinical model. The results show that both SiO₂-AgNP and SiO₂-BiNP composites completely inhibited H. pylori and showed high activity against other pathogens, although P. aeruginosa remained less susceptible. Functionalization of AgNP-coated samples with APTES promoted uniform distribution of AgNPs, with the minimum bactericidal concentration (MBC) to minimum inhibitory concentration (MIC) ratios ranging from 1 to 4, confirming a bactericidal rather than bacteriostatic effect. In contrast, BiNP-coated samples without APTES exhibited lower MIC values from 74 to 595 μg mL⁻¹, consistent with increased Bi³⁺ release from amorphous phases. This indicates the antimicrobial potential, highlighting the role of surface functionalization in regulating ion release and biological performance, and suggesting applications in the biomedical and food industries. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Nanoscience)

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23 pages, 3750 KB

Open AccessArticle

CaP Nanoparticles Improve the Effect of dsRNA on Gene Expression, Growth, and Mycotoxin Production of Toxigenic Fusarium graminearum

by Alexander A. Stakheev, Polina Bagdasarova, Eugene A. Rogozhin, Victoria Tikhomirova, Ekaterina Popova, Assel Akhmetova, Olga Kost, Natalia O. Kalinina, Michael Taliansky and Sergey K. Zavriev

Int. J. Mol. Sci. 2025, 26(20), 10021; https://doi.org/10.3390/ijms262010021 - 15 Oct 2025

Viewed by 238

Abstract

Fusarium species and the mycotoxins produced by them represent a significant problem for agriculture and human health. Thus, the development of novel management strategies and tools is of high importance. Spray-induced gene silencing (SIGS), based on the natural mechanism of RNA interference (RNAi), has been considered as a highly specific and ecologically safe alternative to chemical fungicides, the use of which is restricted by the emergence of resistant strains and environmental concerns. At the same time, massive application of SIGS is challenged by the degradability of RNA molecules in the environment. Nanoparticles have been widely applied to protect RNA from degradation and improve its action. The aims of this study were to evaluate whether RNAi-mediated silencing of the regulatory FgVe1 gene leads to inhibition of growth, mycotoxin production, and pathogenicity of Fusarium graminearum and whether the use of CaP nanoparticles (CaPs) as double-stranded RNA (dsRNA) carriers enhances and prolongs the silencing effect. It was shown that dsRNA treatment of fungal liquid cultures resulted in 19.78-fold silencing of FgVe1 expression as well as inhibition of expression of genes related to secondary metabolism, including those involved in trichothecene and aurofusarin biosynthesis, thus leading to a reduction in DON accumulation and changes in culture color. The results also demonstrated that naked dsRNA and CaPs:dsRNA nanocomplexes differed in their abilities to induce a high silencing effect at different time points. Naked dsRNA proved more effective in inducing silencing in the early stages of fungal growth, whereas application of nanocomplexes provided a prolonged effect up to 10 days in liquid cultures and up to 14 days on detached leaves. The obtained data can be considered as a basis for the further development of new efficient SIGS-based plant protection strategies. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Nanoscience)

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11 pages, 4985 KB

Open AccessArticle

Morphological Characterization of Plasma-Derived Nanoparticles Isolated by High-Speed Ultracentrifugation: A Scanning Electron Microscopy Study

by Lubov A. Kungurova, Alexander A. Artamonov, Evgeniy A. Grigoryev, Aleksei Yu. Aronov, Olga S. Vezo, Ruslan I. Glushakov and Kirill A. Kondratov

Int. J. Mol. Sci. 2025, 26(19), 9422; https://doi.org/10.3390/ijms26199422 - 26 Sep 2025

Viewed by 462

Abstract

Extracellular vesicles are critical mediators of intercellular signaling. Recent studies have revealed that, in addition to vesicular structures, smaller non-vesicular nanoparticles—termed exomeres and supermeres—also participate in intercellular communication. Detailed characterization of these nanoscale entities within biological systems is essential for elucidating their structural and functional roles. Due to their sub-50 nm dimensions, high-resolution imaging modalities such as atomic force microscopy and electron microscopy are currently the primary techniques available for their visualization. In the present study, we employed low-voltage scanning electron microscopy to investigate the size of exomeres and supermeres isolated from human blood plasma via high-speed ultracentrifugation. Platelet-poor plasma was obtained from the blood of six healthy donors (two women and four men, aged 21–46 years). By ultracentrifugation (170,000× g for 4 h), the plasma was purified of extracellular vesicles. Two fractions were sequentially isolated: one containing exomeres (170,000× g for 20 h) and one containing supermeres (370,000× g for 20 h). The particles were examined using a Zeiss Auriga microscope with no sputter coating at an accelerating voltage of 0.4–0.5 kV. The images obtained from the fractions showed particles 10–50 nm in diameter, both individual particles and aggregated structures. The fractions were also slightly contaminated with larger particles, supposedly extracellular vesicles. Examining the fractions using a dynamic light scattering device additionally revealed the presence of particles 10–18 nm in size. It should be noted that the fractions obtained did indeed contain particles measuring 10–50 nm, which corresponds to the size of exomeres and supermeres. Low-voltage scanning electron microscopy allows for examination of the structure of exomeres and supermeres in blood plasma fractions. However, it should be noted that without the use of immunological identification, this method does not allow exomeres and supermeres to be distinguished from accompanying particles. It should also be noted that because the size of exomeres and supermeres is close to the detection threshold of low-voltage scanning electron microscopy, in such studies it is generally only possible to detect the size of these particles. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Nanoscience)

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17 pages, 6805 KB

Open AccessArticle

Ferritin Nanocages Exhibit Unique Structural Dynamics When Displaying Surface Protein

by Monikaben Padariya, Natalia Marek-Trzonkowska and Umesh Kalathiya

Int. J. Mol. Sci. 2025, 26(15), 7047; https://doi.org/10.3390/ijms26157047 - 22 Jul 2025

Viewed by 829

Abstract

Ferritin nanocages with spherical shells carry proteins or antigens that enable their use as highly efficient nanoreactors and nanocarriers. Mimicking the surface Spike (S) receptor-binding domain (RBD) from SARS-CoV-2, ferritin nanocages induce neutralizing antibody production or block viral entry. Herein, by implementing molecular dynamics simulation, we evaluate the efficiency in the interaction pattern (active or alternative sites) of H-ferritin displaying the 24 S RBDs with host-cell-receptor or monoclonal antibodies (mAbs; B38 or VVH-72). Our constructed nanocage targeted the receptor- or antibody-binding interfaces, suggesting that mAbs demonstrate an enhanced binding affinity with the RBD, with key interactions originating from its variable heavy chain. The S RBD interactions with ACE2 and B38 involved the same binding site but led to divergent dynamic responses. In particular, both B38 chains showed that asymmetric fluctuations had a major effect on their engagement with the Spike RBD. Although the receptor increased the binding affinity of VVH-72 for the RBD, the mAb structural orientation on the nanocage remained identical to its conformation when bound to the host receptor. Overall, our findings characterize the essential pharmacophore formed by Spike RBD residues over nanocage molecules, which mediates high-affinity interactions with either binding partner. Importantly, the ferritin-displayed RBD maintained native receptor and antibody binding profiles, positioning it as a promising scaffold for pre-fusion stabilization and protective RBD vaccine design. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Nanoscience)

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