Nanoinformatics, computer applications for nanomedicine

Characterization of nanoparticles

Modeling and simulation

Imaging techniques

Terminologies, ontologies, and standards

Data integration and exchange

System interoperability

Data and text mining for nanomedicine research

Linking nano-information with computerized medical records

Basic and translational research

Networks of international researchers, projects, and laboratories

Education in nanoinformatics

Ethical considerations

© 2023 by the authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license .

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Nanoinformatics primarily deals with these issues, with the support of major organizations such as the U.S. National Science Foundation, the National Cancer Institute, and the European Commission. In this new context, nanoinformatics employs information techniques for the analysis and processing of information regarding the structure, physicochemical characteristics of nanoparticles and nanomaterials, their interaction with the environment, and their applications in nanomedicine (Maojo et al., 2011). These new applications emerge at a time when genomics and personalized medicine are gaining recognition and promising additional perspectives for biomedicine. The term “nanoinformatics” or “biomedical nanoinformatics” or “nanomedical informatics” can also be associated with other nanotechnology applications, but this work will only focus on the biomedical applications of nanodrugs in clinical oncology. According to the opinions of many scientists, nanomedicine is considered a new branch of medicine operating at a different, nano level, which entails significant physical and chemical differences. This poses great challenges for research, medical practice, and economic implications due to the novel toxicotherapeutic relationships at the nanoscale (Thomas, Pappu, & Baker, 2011). In that sense, we can recall what happened around 1995-2001 when bioinformatics contributed to the rapid completion of the Human Genome Project, and we can assume that informatics will also be crucial for progress in the development of nanomedicine. Nanomedicine encompasses a wide range of significant topics with practical and scientific implications, such as early disease detection, including cancer, the ability to achieve highly specific targeted therapies, new molecular imaging methods based on the optical properties of nanoparticles, drug delivery control methods in very small doses, nanorobots for diagnosis and therapy, hyperthermia treatments, and new approaches to overcoming solubility limitations of new or existing drugs (Kim, Rutka, & Chan, 2010; Thomas, 2023; Thapa, & Kim, 2023). In addition to human applications, nanoinformatics is also being developed in various branches of agriculture (Thakur, Kumari, & Dev, 2021;

• 1.    The lack of appropriate standard classifications for nanomaterials.

• 2.    The rapid development of knowledge about numerous complex biological, chemical, and physical processes occurring at the nanoscale.

• 3.    The heterogeneity of information and structure in many scientific papers across various disciplines and sub-disciplines of nanotechnology.

All these issues increase the challenges of applying standard information retrieval methods in the literature without additional knowledge of the specificities within the presented scientific fields and subfields. New computer-based approaches are needed to effectively and efficiently connect information from nanomedicine, while considering the different levels of complexity encompassed in research, development, and application in nanotechnology. In this context, researchers proposed a direction for this field in the first decade of the 21st century (National Science Foundation, 2010).

Perspective for the applications of nanoinformatics

Tools supporting the selection of nanomaterials for medical diagnostics, therapy, or theranostics should be based on several key criteria for nanoparticles, including size, shape, charge, chemical composition, topology, pharmacokinetics, biological activities or toxicity, and others.

Among the most important information expected from such simulations are characterizations and simulations of the behavior of nanoparticles in biological models, the formation of interactions with target molecules in living systems, or the development of new imaging techniques using quantum dots (Network for Computational Nanotechnology, National Science Foundation, 2009; CaNanoLab). Researchers at the University of Talca in Chile, in collaboration with members of the National Cancer Institute-Frederick’s Center for Advanced Biomedical Computing, have developed a database of nanostructure called the Collaboratory for Structural Nanobiology (Collaboratory for Structural Nanobiology).

Education in nanomedicine and nanoinformatics introduces new content from various scientific disciplines, such as the fundamentals of quantum physics and chemistry, new imaging modalities, modeling, and other areas. Experts with knowledge and skills in the application of nanoinformatics will play an important role in facilitating communication between different medical fields in the near future. The first step is undoubtedly the establishment of nanoinformatics infrastructure and the collection, cataloging, annotation, organization, and archiving of available data. The development and expansion of databases, software tools, and nanoparticles, including their physical and chemical properties, 3D structures, toxicity, and biomedical applications, are crucial.

Modern nanomedicine requires new insights beyond current information technology, which is typically focused on collecting, displaying, and connecting heterogeneous information. In this broad multidisciplinary field, several fundamental questions have been recognized that need to be addressed, and one of them is the nanoparticle database. Other issues include diagnostic and therapeutic methods based on new nanomaterials, new models of electronic health records for personalized therapies, databases on the toxic and secondary effects of nanoparticles, and more. As an example, the collection of information on the application of nanoparticles as carriers for the antineoplastic agent doxorubicin (DOX) can be considered. Doxorubicin is an anthracycline antibiotic approved for clinical use as early as 1972. A major problem with the clinical application of this drug is its numerous adverse effects, with cardiotoxicity being the main concern. Over decades of research on this still indispensable chemotherapy drug, various approaches have been developed to reduce cardiotoxicity. One of them is the chemical synthesis of newer derivatives of doxorubicin. Several derivatives of doxorubicin have been developed to improve its pharmacological efficacy or reduce adverse effects. Some of these derivatives include daunorubicin, epirubicin, and idarubicin. However, this approach has not yielded the desired results in clinical practice. Another approach involves the use of cardioprotective agents such as Dexrazoxane, vitamin C, phenolic natural products, organic chelators, and others. In modern clinical practice, a combination of doxorubicin with other antineoplastic agents has been applied for a long time. The approaches mentioned above to address the fundamental problem of high cardiotoxicity have yielded minimal progress. A new strategy in the application of this drug is the synthesis of novel doxorubicin nanoformulations. Table 1 presents different groups of nanoparticles as carriers for doxorubicin.

Table 1. Groups of nanoparticles as carriers for doxorubicin

Various nanocarriers of doxorubicin	References
Gold nanoparticles	26
Polymeric nanoparticles	27
pH-responsive nanocarriers	28
Lipid nanocarriers	29
Magnetic nanocarriers	30
Carbon-based nanocarriers Fullerenes Carbonnanotubes Graphens	31,32
Other nanocarriares	33

Water-soluble polyhydroxylated derivatives of C60 fullerene, such as C60(OH)24 fullereneol, are nanoparticulate molecules capable of self-assembly in biological media, forming stable polyanionic nanoparticles ranging in size from 5 to 90 nm with a charge ranging from -20 to -55 mV, depending on the conditions (Djordjevic et al., 2015; Vraneš et al., 2017). Fullerene-based nanoparticle (FNP) has shown low cytotoxicity in in vitro studies and low acute, subacute, and chronic toxicity in in vivo models using mice and rats (Dragojevic-Simic et al., 2011). FNP exhibits high antioxidant properties in both chemical and biological models (Mirkov et al., 2004; Bogdanović et al., 2004; Trajković et al., 2007; Bogdanović et al., 2008; Milic et al., 2009; Stankov et al., 2013 Vesna et al., 2016 Kojić et al., 2020). FNP also possesses chelating properties, which were the basis for its cardioprotective potential in DOX applications (Đorđević et al., 2009). Moreover, FNP, in the presence of DOX, forms stable nanoparticles that have demonstrated significant cytotoxic effects on various malignant cell lines (Jović et al., 2016; Seke et al., 2016) while causing considerably fewer negative effects on vital organs in in vivo models (Injac et al., 2009a; Injac et al., 2009b; Torres et al., 2010; Milic Djordjevic et al., 2006; Injac et al., 2008a; Injac et al., 2008b; Injac et al., 2008c Borović et al., 2014; Srdjenovic et al., 2010; Vapa et al., 2012; Jacevic et al., 2017; Petrovic et al.,2018).

Conclusion

Computer engineering and the speed of information flow are developing rapidly. We are witnessing that quantum computers will be the leading technology in the near future. Nanotechnology began to be understood only from the middle of the last century, and in the past few decades, many scientific fields and applications based on nanomaterials have been developed. One of these fields is nanomedicine, which is increasingly being applied in clinical practice. A large number of scientific publications, fundamental and clinical studies, patents, numerous presentations at scientific conferences, and other sources provide information in the field of nanomedicine. A major challenge for the scientific community is how to classify and process all this information. Software programs have been developed that can recognize keywords in the field and classify information for both fundamental and applied research in biomedicine and clinical studies. By developing databases in the nano field and related software for simulating the interactions of nanoparticles in living systems, among other things, research time will be shortened, new mechanisms of action will be recommended, and overall resources will be saved. This approach has introduced a new, complex strategy for biomedical applications.

Conflict of interests

We have no known conflictof interest to disclose