Proteomics, nanotechnology and molecular diagnostics

Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.     

The biotechnology and applications of antibody engineering

The exquisite specificity of monoclonal antibodies (MAb) has long provided the potential for creating new reagents for the in vivo delivery of therapeutic drugs or toxins to defined cellular target sites or improved methods of diagnosis. However, many difficulties associated with their production, affinity, specificity, and use in vivo have largely confined their application to research or in vitro diagnostics. This situation is beginning to change with the recent developments in the applied molecular techniques that allow the engineering of the genes that encode antibodies rather than the manipulation of the intact antibodies themselves. Techniques, such as the polymerase chain reaction, have provided essential methods with which to generate and modify the genetic constituents of antibodies, allow their conjugation to toxins or drugs, provide ways of humanizing murine antibodies, and allow discrete modular antigen binding components to be produced. More recent developments of in vitro expression systems and powerful phage surface display technologies will without doubt play a major role in future antibody engineering and in the successful development of new diagnostic and therapeutic antibody-based reagents.     

Analytical nanobiotechnology for medicine diagnostics

The review is concerned with the state-of-the-art and the prospects of development of nanotechnologies in clinical proteomics. Nanotechnology in clinical proteomics is a new medical research direction, dealing with the creation and application of nanodevices for performing proteomic analyses in the clinic. Nanotechnological progress in the field of atomic force microscopy makes it possible to perform clinical studies on the revelation, visualization and identification of protein disease markers, in particular of those with the sensitivity of 10(-17) M that surpasses by several orders the sensitivity of commonly adopted clinical methods. At the same time, implementation of nanotechnological approaches into diagnostics allows for the creation of new diagnostic systems based on the optical, electro-optical, electromechanical and electrochemical nanosensoric elements with high operating speed. The application of nanotechnological approaches to creating nanopore-based devices for express sequencing of the genome is discussed.     

The pinpoint promise of nanoparticle-based drug delivery and molecular diagnosis

Nanotechnology, or systems/device manufacture at the molecular level, is a multidisciplinary scientific field undergoing explosive development. The genesis of nanotechnology can be traced to the promise of revolutionary advances across medicine, communications, genomics and robotics. Without doubt one of the greatest values of nanotechnology will be in the development of new and effective medical treatments (i.e., nanomedicine). This review focuses on the potential of nanomedicine as it specifically relates to (1) the development of nanoparticles for enabling and improving the targeted delivery of therapeutic agents; (2) developing novel and more effective diagnostic and screening techniques to extend the limits of molecular diagnostics providing point-of-care diagnosis and more personalized medicine.     

Biodelivery of a fullerene derivative

Most current nanotoxicology research is focused on examining the influence of nanomaterials at the tissue and cellular levels. To explore these interactions on the molecular level, new carboxyfullerenes interact with transport proteins at the molecular level. The carboxyfullerenes exhibited an unusual mode of binding outside the calyx of beta-lactoglobulin (a typical representative of lipocalin family of barrier liquid proteins). The complexes were studied by various techniques, including mass spectrometry, UV/vis and circular dichroism spectroscopy, chromatographic methods, gel electrophoresis, and dynamic light scattering. The fullerene ligands were transferred from beta-lactoglobulin to human serum albumin (a representative of a blood transport protein), thus providing a model of how fullerene-based nanomaterials interact with biomolecules and are transported in biological systems.     

Gold and silver nanoparticles for clinical diagnostics - From genomics to proteomics

Nanotechnology has prompted researchers to develop new and improved materials aimed at biomedical applications with particular emphasis in diagnostics and therapy. Special interest has been directed at providing enhanced biomolecular diagnostics, including SNP detection gene expression profiles and biomarker characterisation. These strategies have focused on the development of nanoscale devices and platforms that can be used for single molecule characterisation of nucleic acid, DNA or RNA, and protein at an increased rate when compared to traditional techniques. Also, several advances have been reported on DNA analysis in real time, at both high resolution and very high throughputs, suitable for biomedical diagnostics. Here, we shall provide a review of available nanotechnology-based platforms for biomolecular recognition, and their application to molecular diagnostics and genome analysis, with emphasis on the use of noble metal nanoparticles for simple and specific analysis systems. Particular focus will be put on those already being translated into clinical settings. This article is part of a Special Issue entitled: Proteomics: The clinical link.     

Smart materials on the way to theranostic nanorobots: Molecular machines and nanomotors,advanced biosensors,and intelligent vehicles for drug delivery

BackgroundTheranostics, a fusion of two key parts of modern medicine - diagnostics and therapy of the organism's disorders, promises to bring the efficacy of medical treatment to a fundamentally new level and to become the basis of personalized medicine. Extrapolating today's progress in the field of smart materials to the long-run prospect, we can imagine future intelligent agents capable of performing complex analysis of different physiological factors inside the living organism and implementing a built-in program thereby triggering a series of therapeutic actions. These agents, by analogy with their macroscopic counterparts, can be called nanorobots. It is quite obscure what these devices are going to look like but they will be more or less based on today's achievements in nanobiotechnology.Scope of ReviewThe present Review is an attempt to systematize highly diverse nanomaterials, which may potentially serve as modules for theranostic nanorobotics, e.g., nanomotors, sensing units, and payload carriers.Major ConclusionsBiocomputing-based sensing, externally actuated or chemically “fueled” autonomous movement, swarm inter-agent communication behavior are just a few inspiring examples that nanobiotechnology can offer today for construction of truly intelligent drug delivery systems.General SignificanceThe progress of smart nanomaterials toward fully autonomous drug delivery nanorobots is an exciting prospect for disease treatment. Synergistic combination of the available approaches and their further development may produce intelligent drugs of unmatched functionality.     

DNA-mounted self-assembly: new approaches for genomic analysis and SNP detection

This article presents an overview of new emerging approaches for nucleic acid detection via hybridization techniques that can potentially be applied to genomic analysis and SNP identification in clinical diagnostics. Despite the availability of a diverse variety of SNP genotyping technologies on the diagnostic market, none has truly succeeded in dominating its competitors thus far. Having been designed for specific diagnostic purposes or clinical applications, each of the existing bio-assay systems (briefly outlined here) is usually limited to a relatively narrow aspect or format of nucleic acid detection, and thus cannot entirely satisfy all the varieties of commercial requirements and clinical demands. This drives the diagnostic sector to pursue novel, cost-effective approaches to ensure rapid and reliable identification of pathogenic or hereditary human diseases. Hence, the purpose of this review is to highlight some new strategic directions in DNA detection technologies in order to inspire development of novel molecular diagnostic tools and bio-assay systems with superior reliability, reproducibility, robustness, accuracy and sensitivity at lower assay cost. One approach to improving the sensitivity of an assay to confidently discriminate between single point mutations is based on the use of target assembled, split-probe systems, which constitutes the main focus of this review.     

Interplay between apoptotic and autophagy pathways after exposure to cerium dioxide nanoparticles in human monocytes

Engineered nanomaterials, defined as having at least one dimension smaller than 100 nm, have revolutionized many technology sectors ranging from therapeutics and diagnostics to environmental monitoring and remediation. This has resulted in a rapid increase in their manufacture over the past few years, accompanied by an increased human exposure potential. However, understanding of the interactions of nanomaterials with biological systems is still rudimentary. We have described that an environmentally and medically relevant nano metal (cerium dioxide) can affect primary human monocyte viability and interact with programmed cell death pathways leading to apoptosis and autophagic cell death. Cerium dioxide nanoparticles (CeO₂ NPs)-induced autophagy acts as a prodeath mechanism and leads to increased cytotoxicity of human monocytes. A better understanding of the implication and biological significance of CeO₂ NPs-induced autophagy and apoptosis will help us understand the risks associated with its uses and develop safer nanomedicine.     

Diagnosis of human sleeping sickness: sense and sensitivity

In 1997 the World Health Organization (WHO) advocated increased access to diagnosis and treatment, as well as reinforcement of surveillance, for the control of sleeping sickness (human African trypanosomiasis, HAT). This coincided with the end of decades of civil conflicts in several endemic regions and negotiation of a sustainable supply of 'free' curative drugs and, as a result, HAT is at its lowest level in 50 years. However, reported cases underestimate prevalence and downplay HAT when compared with data generated by advanced diagnostic capacity for human immunodeficiency virus (HIV), tuberculosis (TB) and malaria, and, because HAT case numbers fall between epidemics, diagnostics become less commercially appealing. Here recent trends in the development of diagnostics for sleeping sickness are considered and progress towards a much-needed sensitive, specific and affordable point-of-care diagnostic is assessed.     

Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations

The ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a severe threat to human health and the global economy and has resulted in overwhelming stress on health care systems worldwide. Despite the global health catastrophe, especially in the number of infections and fatalities, the COVID-19 pandemic has also revolutionized research and discovery with remarkable success in diagnostics, treatments, and vaccine development. The use of many diagnostic methods has helped establish public health guidelines to mitigate the spread of COVID-19. However, limited information has been shared about these methods, and there is a need for the scientific community to learn about these technologies, in addition to their sensitivity, specificity, and limitations. This review article is focused on providing insights into the major methods used for SARS-CoV-2 detection. We describe in detail the core principle of each method, including molecular and serological approaches, along with reported claims about the rates of false negatives and false positives, the types of specimens needed, and the level of technology and the time required to perform each test. Although this study will not rank or prioritize these methods, the information will help in the development of guidelines and diagnostic protocols in clinical settings and reference laboratories.     

Molecularly imprinted polymers for the recognition of proteins: the state of the art

Molecular imprinting has proved to be an effective technique for the creation of recognition sites on a polymer scaffold. Protein imprinting has been a focus for many chemists working in the area of molecular recognition, since the creation of synthetic polymers that can specifically recognise proteins is a very challenging but potentially extremely rewarding objective. It is expected that molecularly imprinted polymers (MIPs) with specificity for proteins will find application in medicine, diagnostics, proteomics, environmental analysis, sensors and drug delivery. In this review, the authors provide an overview of the progress achieved in the decade between 1994 and 2005, with respect to the challenging area of MIPs for protein recognition. The discussion furnishes a comparative analysis of different approaches developed, underlining their relative advantages and disadvantages and highlighting trends and possible future directions.     

New understanding of the group A Streptococcus pathogenesis cycle

Group A Streptococcus (GAS) has long been recognized as a human pathogen causing an exceptionally broad range of infections. Despite intense research, however, the molecular mechanisms of GAS disease remain unclear. Recently, many important discoveries have been made that shed light on GAS pathogenesis and open exciting avenues for future research. Advances in genome sequencing, microarray technology and proteomic analysis, in combination with the development of more suitable animal models, have markedly increased our knowledge of the mechanisms underlying GAS pathogenesis. The information gained from these studies will translate into improved diagnostics and new targets for therapeutic drugs and vaccines.     

Mass spectrometry of nucleic acids in molecular medicine

A stable streamlining trend in the field of medical diagnostics by practical adoption of high-tech and knowledge-intensive analytical systems providing for molecular level studies has appeared during the last few decades. An illustrative example of such technologies is mass spectrometry methods for analyzing biomolecules. This review is intended to brief the potential of the state-of-the-art inventory of spectrometry equipment and illustrate the application of mass spectrometry of nucleic acids (DNA and RNA) for solving practical problems related to the analysis of human genomic DNA and clinically significant microorganisms of bacterial and viral natures.     

New trends in microbial technology

Microbial technology includes not only the production of materials in bioreactors, or the production of new catalysts by genetic engineering but extends to aspects of both human and animal health care, waste and pollution management, enhanced oil recovery, mineral leaching, advanced plant breeding, diagnostics and analytical equipment, biosensors, bioelectronics and renewable energy system based on biomass feedstocks. National strategies of industrialized countries are being developed which identify microbial technology as a substantial factor in the attainment of industrial and economic goals. Although extremely promising microbial technology is not a quick fix and its application will only arise as a result of systematic programme of research and development. Such programme requires a broad base of disciplinary underpinning in molecular biology, genetics and bioengineering. The development of expertise of this kind in the tertiary educational institutions is the essential starting point. It should be developed by appropriate programmes and networking systems.     

Emerging biological materials through molecular self-assembly

Understanding of new materials at the molecular level has become increasingly critical for a new generation of nanomaterials for nanotechnology, namely, the design, synthesis and fabrication of nanodevices at the molecular scale. New technology through molecular self-assembly as a fabrication tool will become tremendously important in the coming decades. Basic engineering principles for microfabrication can be learned by understanding the molecular self-assembly phenomena. Self-assembly phenomenon is ubiquitous in nature. The key elements in molecular self-assembly are chemical complementarity and structural compatibility through noncovalent interactions. We have defined the path to understand these principles. Numerous self-assembling systems have been developed ranging from models to the study of protein folding and protein conformational diseases, to molecular electronics, surface engineering, and nanotechnology. Several distinctive types of self-assembling peptide systems have been developed. Type I, "molecular Lego" forms a hydrogel scaffold for tissue engineering; Type II, "molecular switch" as a molecular actuator; Type III, "molecular hook" and "molecular velcro" for surface engineering; Type IV, peptide nanotubes and nanovesicles, or "molecular capsule" for protein and gene deliveries and Type V, "molecular cavity" for biomineralization. These self-assembling peptide systems are simple, versatile and easy to produce. These self-assembly systems represent a significant advance in the molecular engineering for diverse technological innovations.     

Utilization of monoclonal antibody-targeted nanomaterials in the treatment of cancer

Due to their excellent specificity for a single epitope, monoclonal antibodies (mAbs) present a means of influencing the function of cells at the molecular level. In particular they show great promise in the treatment of cancer because they can inhibit cancer cell proliferation, tumor angiogenesis, invasiveness and malignant spread of cancerous cells. Many mAbs are in various stages of testing and 11 are currently marketed in the US or Europe for the treatment of cancers that express particular antigens such as human epidermal growth factor receptor-2, CD20, epidermal growth factor receptor and vascular endothelial growth factor. Strategies to conjugate mAbs to toxins, radioactive isotopes and chemotherapeutic drugs to improve efficacy are under intense investigation and numerous immunoconjugates have been studied in the clinical setting. However, the molecules have limitations, and so nanomaterials (NMs), which potentially offer more flexibility of design and functionality in providing platforms for binding of multiple therapeutic agents in a single structure, are being examined as an alternative. Studies utilizing mAb-targeted NMs have shown that they exhibit focused targeting, improved pharmacokinetics and improved “passive” drug delivery via leaky vasculature. Nevertheless, before they can be utilized to treat cancer, potential NM toxicity must be thoroughly investigated. Thus, rigorous testing of NM-mAb conjugates in both in vitro and in vivo systems is underway to determine how NM-mAb conjugates will interact with cells and tissues of the body. In this review, we discuss the broad range of nanomaterials that are under investigation as potential platforms for the presentation of mAbs either as single therapeutics or in combination with other drugs and their advantages and limitations in specifically targeting cancer.     

Molecular aptamers for drug delivery

The active targeting of drugs in a cell-, tissue- or disease-specific manner represents a potentially powerful technology with widespread applications in medicine, including the treatment of cancers. Aptamers have properties such as high affinity and specificity for targets, easy chemical synthesis and modification, and rapid tissue penetration. They have become attractive molecules in diagnostics and therapeutics rivaling and, in some cases, surpassing other molecular probes, such as antibodies. In this review, we highlight the recent progress in aptamer-mediated delivery for therapeutics and disease-targeting based on aptamer integration with a variety of nanomaterials, such as gold nanorods, DNA micelles, DNA hydrogels and carbon nanotubes.