Submit to Molecules Review for Molecules Propose a Special Issue

Journal Browser

► Journal Browser

Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment

Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Nanochemistry".

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 22724

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment book cover image

Share This Special Issue

Special Issue Editor

Prof. Dr. Jahir Orozco Holguín

E-Mail Website
Guest Editor

Max Planck Tandem Group in Nanobioengineering, Universidad de Antioquia, Antioquia, Colombia
Interests: nano-bioengineering; nanomotors; micro(nano)carriers; nano-encapsulation; selective and controlled drug delivery; chemical (bio)sensors and nano(micro)devices; electrochemistry

Special Issue Information

Dear Colleagues,

Nanobioengineering converges at the frontier of basic sciences, engineering, and technology, searching for new or existing (bio)molecules and materials, understanding their interactions, and providing novel functionalities for new products and unexpected applications. Nanobioengineering offers outstanding opportunities for developing innovative platforms with potential use in prevention, diagnostics, and therapeutics within the health care field. For example, nanobioprobes and nanobioconjugates may provide alternatives for the prevention and convenient real-time diagnosis of diseases closer to the patient, and opportunities for more efficient drug delivery and targeted therapeutics compared with conventional technologies. In this context, the rational design of biological structures and/or their assembly with nanomaterials allows the on-demand development of nanobioengineered platforms with improved properties and outstanding performance, which, acting alone or in synergy, are paving the way towards a new paradigm of personalized medicine.

This Special Issue covers recent research in the field of nanobioengineering convergence, and aims to provide a platform for studies on new (bio)molecules, hybrids and extracts with nutraceutical or therapeutical properties, novel nanobioengineered biosensors for disease diagnostics, and nanoparticles and nanobioconjugates for targeted drug delivery. This Special Issue is focused on (but not limited to) research in cancer and infectious diseases with an impact on health care. Contributions in the form of original research papers, short communications, and reviews are welcome.

Prof. Dr. Jahir Orozco Holguín
Guest Editor

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. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

nanobioengineering
nanobiosensors
nanocarriers
(bio)molecules
hybrids
extracts
nutraceuticals
drug delivery
diagnosis
theranostics
treatment
cancer
infectious diseases

Published Papers (11 papers)

Download All Papers

Research

Jump to: Review

13 pages, 2049 KiB

Open AccessArticle

Selecting Nanobodies Specific for the Epidermal Growth Factor from a Synthetic Nanobody Library

by Yunier Serrano-Rivero, Julieta Salazar-Uribe, Marcela Rubio-Carrasquilla, Frank Camacho-Casanova, Oliberto Sánchez-Ramos, Alaín González-Pose and Ernesto Moreno

Molecules 2023, 28(10), 4043; https://doi.org/10.3390/molecules28104043 - 12 May 2023

Viewed by 1831

Abstract

The epidermal growth factor (EGF) is one of the most critical ligands of the EGF receptor (EGFR), a well-known oncogene frequently overexpressed in cancerous cells and an important therapeutic target in cancer. The EGF is the target of a therapeutic vaccine aimed at inducing an anti-EGF antibody response to sequester this molecule from serum. However, strikingly, very few investigations have focused on EGF immunotargeting. Since the use of nanobodies (Nbs) for EGF neutralization may be an effective therapeutic strategy in several types of cancer, in this study, we decided to generate anti-EGF Nbs from a recently constructed, phage-displaying synthetic nanobody library. To our knowledge, this is the first attempt to obtain anti-EGF Nbs from a synthetic library. By applying a selection strategy that uses four different sequential elution steps along with three rounds of selection, we obtained four different EGF-specific Nb clones, and also tested their binding capabilities as recombinant proteins. The obtained results are very encouraging and demonstrate the feasibility of selecting nanobodies against small antigens, such as the EGF, from synthetic libraries. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

17 pages, 7329 KiB

Open AccessArticle

Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs

by Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Daiver E. Jiménez-Gutiérrez and Ernesto Moreno

Molecules 2023, 28(10), 3991; https://doi.org/10.3390/molecules28103991 - 9 May 2023

Cited by 4 | Viewed by 2610

Abstract

The number of applications for nanobodies is steadily expanding, positioning these molecules as fast-growing biologic products in the biotechnology market. Several of their applications require protein engineering, which in turn would greatly benefit from having a reliable structural model of the nanobody of interest. However, as with antibodies, the structural modeling of nanobodies is still a challenge. With the rise of artificial intelligence (AI), several methods have been developed in recent years that attempt to solve the problem of protein modeling. In this study, we have compared the performance in nanobody modeling of several state-of-the-art AI-based programs, either designed for general protein modeling, such as AlphaFold2, OmegaFold, ESMFold, and Yang-Server, or specifically designed for antibody modeling, such as IgFold, and Nanonet. While all these programs performed rather well in constructing the nanobody framework and CDRs 1 and 2, modeling CDR3 still represents a big challenge. Interestingly, tailoring an AI method for antibody modeling does not necessarily translate into better results for nanobodies. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

14 pages, 2671 KiB

Open AccessArticle

Design and Construction of a Synthetic Nanobody Library: Testing Its Potential with a Single Selection Round Strategy

by María Angélica Contreras, Yunier Serrano-Rivero, Alaín González-Pose, Julieta Salazar-Uribe, Marcela Rubio-Carrasquilla, Matheus Soares-Alves, Natalie C. Parra, Frank Camacho-Casanova, Oliberto Sánchez-Ramos and Ernesto Moreno

Molecules 2023, 28(9), 3708; https://doi.org/10.3390/molecules28093708 - 25 Apr 2023

Cited by 4 | Viewed by 3210

Abstract

Nanobodies (Nbs) are single domain antibody fragments derived from heavy-chain antibodies found in members of the Camelidae family. They have become a relevant class of biomolecules for many different applications because of several important advantages such as their small size, high solubility and stability, and low production costs. On the other hand, synthetic Nb libraries are emerging as an attractive alternative to animal immunization for the selection of antigen-specific Nbs. Here, we present the design and construction of a new synthetic nanobody library using the phage display technology, following a structure-based approach in which the three hypervariable loops were subjected to position-specific randomization schemes. The constructed library has a clonal diversity of 10⁸ and an amino acid variability that matches the codon distribution set by design at each randomized position. We have explored the capabilities of the new library by selecting nanobodies specific for three antigens: vascular endothelial growth factor (VEGF), tumor necrosis factor (TNF) and the glycoprotein complex (GnGc) of Andes virus. To test the potential of the library to yield a variety of antigen-specific Nbs, we introduced a biopanning strategy consisting of a single selection round using stringent conditions. Using this approach, we obtained several binders for each of the target antigens. The constructed library represents a promising nanobody source for different applications. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

17 pages, 3097 KiB

Open AccessArticle

Identifying Potential Molecular Targets in Fungi Based on (Dis)Similarities in Binding Site Architecture with Proteins of the Human Pharmacolome

by Johann E. Bedoya-Cardona, Marcela Rubio-Carrasquilla, Iliana M. Ramírez-Velásquez, Mario S. Valdés-Tresanco and Ernesto Moreno

Molecules 2023, 28(2), 692; https://doi.org/10.3390/molecules28020692 - 10 Jan 2023

Viewed by 2084

Abstract

Invasive fungal infections represent a public health problem that worsens over the years with the increasing resistance to current antimycotic agents. Therefore, there is a compelling medical need of widening the antifungal drug repertoire, following different methods such as drug repositioning, identification and validation of new molecular targets and developing new inhibitors against these targets. In this work we developed a structure-based strategy for drug repositioning and new drug design, which can be applied to infectious fungi and other pathogens. Instead of applying the commonly accepted off-target criterion to discard fungal proteins with close homologues in humans, the core of our approach consists in identifying fungal proteins with active sites that are structurally similar, but preferably not identical to binding sites of proteins from the so-called “human pharmacolome”. Using structural information from thousands of human protein target-inhibitor complexes, we identified dozens of proteins in fungal species of the genera Histoplasma, Candida, Cryptococcus, Aspergillus and Fusarium, which might be exploited for drug repositioning and, more importantly, also for the design of new fungus-specific inhibitors. As a case study, we present the in vitro experiments performed with a set of selected inhibitors of the human mitogen-activated protein kinases 1/2 (MEK1/2), several of which showed a marked cytotoxic activity in different fungal species. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

19 pages, 13445 KiB

Open AccessArticle

Computational Simulation of Colorectal Cancer Biomarker Particle Mobility in a 3D Model

by Esteban Vallejo Morales, Gustavo Suárez Guerrero and Lina M. Hoyos Palacio

Molecules 2023, 28(2), 589; https://doi.org/10.3390/molecules28020589 - 6 Jan 2023

Viewed by 1528

Abstract

Even though some methods for the detection of colorectal cancer have been used clinically, most of the techniques used do not consider the in situ detection of colorectal cancer (CRC) biomarkers, which would favor in vivo real-time monitoring of the carcinogenesis process and consequent studies of the disease. In order to give a scientific and computational framework ideal for the evaluation of diagnosis techniques based on the early detection of biomarker molecules modeled as spherical particles from the computational point of view, a computational representation of the rectum, stool and biomarker particles was developed. As consequence of the transport of stool, there was a displacement of CRC biomarker particles that entered the system as a result of the cellular apoptosis processes in polyps with a length lower than 1 cm, reaching a maximum velocity of

3.47 \times 10^{- 3}

m/s. The biomarkers studied showed trajectories distant to regions of the polyp of origin in 1 min of simulation. The research results show that the biomarker particles for CRC respond to the variations in the movements of the stool with trajectories and speeds that depend on the location of the injury, which will allow locating the regions with the highest possibilities of catching particles through in situ measurement instruments in the future. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

14 pages, 4643 KiB

Open AccessArticle

Site-Directed Mutants of Parasporin PS2Aa1 with Enhanced Cytotoxic Activity in Colorectal Cancer Cell Lines

by Miguel O. Suárez-Barrera, Lydia Visser, Efraín H. Pinzón-Reyes, Paola Rondón Villarreal, Juan S. Alarcón-Aldana and Nohora Juliana Rueda-Forero

Molecules 2022, 27(21), 7262; https://doi.org/10.3390/molecules27217262 - 26 Oct 2022

Viewed by 1849

Abstract

Parasporin 2 has cytotoxic effects against numerous colon cancer cell lines, making it a viable alternative to traditional treatments. However, its mechanism of action and receptors remain unknown. In this study, site-directed mutagenesis was used to obtain PS2Aa1 mutants with variation in domain I at positions 256 and 257. Variants 015, 002, 3-3, 3-35, and 3-45 presented G256A, G256E, G257A, G257V, and G257E substitutions, respectively. Cytotoxicity tests were performed for the cell viability of cell lines SW480, SW620, and CaCo-2. Mutants 3-3, 3-35, and 3-45 efficiently killed the cell lines. It was found that the activated forms of caspase-3 and PARP were in higher abundance as well as increased production of γH2AX when 3-35 was used to treat CaCo-2 and SW480. To assess possible membrane-binding receptors involved in the interaction, an APN receptor blocking assay showed reduced activity of some parasporins. Hence, we performed molecular docking and molecular dynamics simulations to analyze the stability of possible interactions and identify the residues that could be involved in the protein–protein interaction of PS2Aa1 and APN. We found that residues 256 and 257 facilitate the interaction. Parasporin 3-35 is promising because it has higher cytotoxicity than PS2Aa1. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

22 pages, 9069 KiB

Open AccessArticle

Development of Genistein Drug Delivery Systems Based on Bacterial Nanocellulose for Potential Colorectal Cancer Chemoprevention: Effect of Nanocellulose Surface Modification on Genistein Adsorption

by Melissa Castaño, Estefanía Martínez, Marlon Osorio and Cristina Castro

Molecules 2022, 27(21), 7201; https://doi.org/10.3390/molecules27217201 - 24 Oct 2022

Cited by 9 | Viewed by 1791

Abstract

Genistein is an isoflavone with antioxidant, anti-inflammatory, and anticancer properties. That said, its use in the industry is limited by its low solubility in aqueous systems. In this work, bacterial nanocellulose (BNC) and BNC modified with cetyltrimethylammonium (BNC-CTAB) were evaluated as genistein-encapsulating materials for their controlled release in cancer chemoprevention. Thin films were obtained and characterized by contact angle, AFM, TEM, UV–Vis spectroscopy FTIR, and TGA techniques to verify surface modification and genistein encapsulation. The results show a decrease in hydrophilization degree and an increase in diameter after BNC modification. Furthermore, the affinity of genistein with the encapsulating materials was determined in the context of monolayer and multilayer isotherms, thermodynamic parameters and adsorption kinetics. Spontaneous, endothermic and reversible adsorption processes were found for BNC-GEN and BNC-CTAB-GEN. After two hours, the maximum adsorption capacity corresponded to 4.59 mg GEN∙g⁻¹ BNC and 6.10 mg GEN∙g⁻¹ BNC-CTAB; the latter was a more stable system. Additionally, in vitro release assays performed with simulated gastrointestinal fluids indicated controlled and continuous desorption in gastric and colon fluids, with a release of around 5% and 85%, respectively, for either system. Finally, the IC50 tests made it possible to determine the amounts of films required to achieve therapeutic concentrations for SW480 and SW620 cell lines. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

19 pages, 2875 KiB

Open AccessArticle

Chemopreventive Effect on Human Colon Adenocarcinoma Cells of Styrylquinolines: Synthesis, Cytotoxicity, Proapoptotic Effect and Molecular Docking Analysis

by Vanesa Bedoya-Betancur, Elizabeth Correa, Juan Pablo Rendón, Andrés F. Yepes-Pérez, Wilson Cardona-Galeano and Tonny W. Naranjo

Molecules 2022, 27(20), 7108; https://doi.org/10.3390/molecules27207108 - 21 Oct 2022

Cited by 2 | Viewed by 1251

Abstract

Seven styrylquinolines were synthesized in this study. Two of these styrylquinolines are new and were elucidated by spectroscopic analysis. The chemopreventive potential of these compounds was evaluated against SW480 human colon adenocarcinoma cells, its metastatic derivative SW620, and normal cells (HaCaT). According to the results, compounds 3a and 3d showed antiproliferative activity in SW480 and SW620 cells, but their effect seemed to be caused by different mechanisms of action. Compound 3a induced apoptosis independent of ROS production, as evidenced by increased levels of caspase 3, and had an immunomodulatory effect, positively regulating the production of different immunological markers in malignant cell lines. In contrast, compound 3d generated a pro-oxidant response and inhibited the growth of cancer cells, probably by another type of cell death other than apoptosis. Molecular docking studies indicated that the most active compound, 3a, could efficiently bind to the proapoptotic human caspases-3 protein, a result that could provide valuable information on the biochemical mechanism for the in vitro cytotoxic response of this compound in SW620 colon carcinoma cell lines. The obtained results suggest that these compounds have chemopreventive potential against CRC, but more studies should be carried out to elucidate the molecular mechanisms of action of each of them in depth. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

20 pages, 3581 KiB

Open AccessArticle

Evaluation of the Effects of Genistein In Vitro as a Chemopreventive Agent for Colorectal Cancer—Strategy to Improve Its Efficiency When Administered Orally

by Juan Pablo Rendón, Ana Isabel Cañas, Elizabeth Correa, Vanesa Bedoya-Betancur, Marlon Osorio, Cristina Castro and Tonny W. Naranjo

Molecules 2022, 27(20), 7042; https://doi.org/10.3390/molecules27207042 - 19 Oct 2022

Cited by 9 | Viewed by 1778

Abstract

Colorectal Cancer (CRC) ranks third in terms of incidence and second in terms of mortality and prevalence worldwide. In relation to chemotherapy treatment, the most used drug is 5-fluorouracil (5-FU); however, the use of this drug generates various toxic effects at the systemic level. For this reason, new therapeutic strategies are currently being sought that can be used as neoadjuvant or adjuvant treatments. Recent research has shown that natural compounds, such as genistein, have chemotherapeutic and anticancer effects, but the mechanisms of action of genistein and its molecular targets in human colon cells have not been fully elucidated. The results reported in relation to non-malignant cell lines are also unclear, which does not allow evidence of the selectivity that this compound may have. Therefore, in this work, genistein was evaluated in vitro in both cancer cell lines SW480 and SW620 and in the non-malignant cell line HaCaT. The results obtained show that genistein has selectivity for the SW480 and SW620 cell lines. In addition, it inhibits cell viability and has an antiproliferative effect in a dose-dependent manner. Increased production of reactive oxygen species (ROS) was also found, suggesting an association with the cell death process through various mechanisms. Finally, the encapsulation strategy that was proposed made it possible to demonstrate that bacterial nanocellulose (BNC) is capable of protecting genistein from the acidic conditions of gastric fluid and also allows the release of the compound in the colonic fluid. This would allow genistein to act locally in the mucosa of the colon where the first stages of CRC occur. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

Review

Jump to: Research

27 pages, 2942 KiB

Open AccessReview

Glycan-Based Electrochemical Biosensors: Promising Tools for the Detection of Infectious Diseases and Cancer Biomarkers

by Danilo Echeverri and Jahir Orozco

Molecules 2022, 27(23), 8533; https://doi.org/10.3390/molecules27238533 - 3 Dec 2022

Cited by 7 | Viewed by 2772

Abstract

Glycan-based electrochemical biosensors are emerging as analytical tools for determining multiple molecular targets relevant to diagnosing infectious diseases and detecting cancer biomarkers. These biosensors allow for the detection of target analytes at ultra-low concentrations, which is mandatory for early disease diagnosis. Nanostructure-decorated platforms have been demonstrated to enhance the analytical performance of electrochemical biosensors. In addition, glycans anchored to electrode platforms as bioreceptors exhibit high specificity toward biomarker detection. Both attributes offer a synergy that allows ultrasensitive detection of molecular targets of clinical interest. In this context, we review recent advances in electrochemical glycobiosensors for detecting infectious diseases and cancer biomarkers focused on colorectal cancer. We also describe general aspects of structural glycobiology, definitions, and classification of electrochemical biosensors and discuss relevant works on electrochemical glycobiosensors in the last ten years. Finally, we summarize the advances in electrochemical glycobiosensors and comment on some challenges and limitations needed to advance toward real clinical applications of these devices. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures

Figure 1

16 pages, 862 KiB

Open AccessReview

Formation of miRNA Nanoprobes—Conjugation Approaches Leading to the Functionalization

by Iveta Vilímová, Katel Hervé-Aubert and Igor Chourpa

Molecules 2022, 27(23), 8428; https://doi.org/10.3390/molecules27238428 - 2 Dec 2022

Viewed by 1380

Abstract

Recently, microRNAs (miRNA) captured the interest as novel diagnostic and prognostic biomarkers, with their potential for early indication of numerous pathologies. Since miRNA is a short, non-coding RNA sequence, the sensitivity and selectivity of their detection remain a cornerstone of scientific research. As such, methods based on nanomaterials have emerged in hopes of developing fast and facile approaches. At the core of the detection method based on nanotechnology lie nanoprobes and other functionalized nanomaterials. Since miRNA sensing and detection are generally rooted in the capture of target miRNA with the complementary sequence of oligonucleotides, the sequence needs to be attached to the nanomaterial with a specific conjugation strategy. As each nanomaterial has its unique properties, and each conjugation approach presents its drawbacks and advantages, this review offers a condensed overview of the conjugation approaches in nanomaterial-based miRNA sensing. Starting with a brief recapitulation of specific properties and characteristics of nanomaterials that can be used as a substrate, the focus is then centered on covalent and non-covalent bonding chemistry, leading to the functionalization of the nanomaterials, which are the most commonly used in miRNA sensing methods. Full article

(This article belongs to the Special Issue Converging Nanochemistry: From Disease Prevention to Diagnosis and Treatment)

► Show Figures